TLE3 as a marker for chemotherapy

ABSTRACT

Methods of using TLE3 as a marker for predicting the likelihood that a patient&#39;s cancer will respond to chemotherapy. Methods of using TLE3 as a marker for selecting a chemotherapy for a cancer.

CROSS REFERENCE TO RELATED APPLICATION

This application is a continuation of U.S. patent application Ser. No.12/277,920, filed Nov. 25, 2008, which claims priority to U.S.Provisional Patent Application Ser. No. 60/991,487, filed Nov. 30, 2007,both of which are hereby incorporated herein by reference in theirentireties.

SEQUENCE LISTING

In accordance with 37 C.F.R. §1.52(e)(5), a Sequence Listing in the formof a text file (entitled “Sequence Listing.txt,” created on Oct. 13,2009, and 90 kilobytes) is incorporated herein by reference in itsentirety.

BACKGROUND OF THE INVENTION

A major challenge of cancer treatment is the selection of chemotherapiesthat maximize efficacy and minimize toxicity for a given patient. Assaysfor cell surface markers, e.g., using immunohistochemistry (IHC), haveprovided means for dividing certain cancers into subclasses. Forexample, one factor considered in prognosis and treatment decisions forbreast cancer is the presence or absence of the estrogen receptor (ER).ER-positive breast cancers typically respond much more readily tohormonal therapies such as tamoxifen, which acts as an anti-estrogen inbreast tissue, than ER-negative cancers. Though useful, these analysesonly in part predict the clinical behavior of breast cancers. There isphenotypic diversity present in cancers that current diagnostic toolsfail to detect. As a consequence, there is still much controversy overhow to stratify patients amongst potential treatments in order tooptimize outcome (e.g., for breast cancer see “NIH Consensus DevelopmentConference Statement: Adjuvant Therapy for Breast Cancer, Nov. 1-3,2000”, J. Nat. Cancer Inst. Monographs, 30:5-15, 2001 and Di Leo et al.,Int. J. Clin. Oncol. 7:245-253, 2002). In particular, there is currentlyno tool for predicting a patient's likely response to treatment withpaclitaxel, a chemotherapeutic with particularly adverse side-effects.There clearly exists a need for improved methods and reagents forclassifying cancers and thereby selecting therapeutic regimens thatmaximize efficacy and minimize toxicity for a given patient.

SUMMARY OF THE INVENTION

We have identified a correlation between the expression of TLE3(transducin-like enhancer of split 3, Entrez Gene ID 7090) and acancer's response to chemotherapy. This correlation has beendemonstrated using TLE3 antibodies and samples from breast cancercohorts which include both treated and untreated patients with knownoutcome. The inventors have also observed that binding of TLE3antibodies in samples from treated ovarian cancer patients correlateswith improved prognosis. In one aspect, the present invention thereforeprovides methods of using TLE3 as a marker for predicting the likelihoodthat a patient's cancer will respond to chemotherapy. In another aspect,the present invention provides methods of using TLE3 as a marker fordeciding whether to administer chemotherapy to a cancer patient. In yetanother aspect, the present invention provides methods of using TLE3 asa marker for selecting a chemotherapy for a cancer patient.

Expression of TLE3 can be detected using any known method. Thus, whilethe inventive methods have been exemplified by detecting TLE3polypeptides using antibodies, in certain embodiments TLE3polynucleotides may be detected using one or more primers as is wellknown in the art.

In general, TLE3 can be used in conjunction with other markers orclinical factors (e.g., stage, tumor size, node characteristics, age,etc.) to further improve the predictive power of the inventive methods.

BRIEF DESCRIPTION OF THE APPENDIX

This patent application refers to material comprising a table and datapresented as Appendix A immediately after the section entitled“Exemplification” and immediately before the section entitled “OtherEmbodiments.” Specifically, Appendix A is a table that lists a varietyof markers that could be used in a panel in conjunction with the TLE3marker in an inventive method. The table includes the antibody ID,parent gene name, Entrez Gene ID, known aliases for the parent gene,peptides that may be used in preparing antibodies and exemplary antibodytiters for staining Using the parent gene name, Entrez Gene ID and/orknown aliases for the parent gene, a skilled person can readily obtainthe nucleotide (and corresponding amino acid) sequences for each andevery one of the parent genes that are listed in Appendix A from apublic database (e.g., GenBank, Swiss-Prot or any future derivative ofthese). The nucleotide and corresponding amino acid sequences for eachand every one of the parent genes that are listed in Appendix A arehereby incorporated by reference from these public databases. Antibodieswith IDs that begin with S5 or S6 may be obtained from commercialsources as indicated.

BRIEF DESCRIPTION OF THE DRAWING

FIG. 1 compares IHC images of TLE3-negative (S0643−) and TLE3-positive(S06430+) samples from breast cancer patients.

FIG. 2 shows Kaplan-Meier recurrence curves that were generated usingall patients in the Huntsville Hospital (HH) breast cancer cohort afterclassification based on staining with an antibody raised against theTLE3 marker. Recurrence data from TLE3-positive and TLE3-negativepatients were used to generate the top and bottom curves, respectively.As shown in the Figure, antibody binding to the TLE3 marker correlateswith improved prognosis across this breast cancer cohort (HR=0.573,p<0.004).

FIG. 3 shows Kaplan-Meier recurrence curves that were generated usingall patients in the Roswell Park Cancer Institute (RP) breast cancercohort after classification based on staining with an antibody raisedagainst the TLE3 marker. The selected patients in the RP cohort were alltriple negative for the ER (estrogen receptor, Entrez GeneID 2099), PR(progesterone receptor, Entrez GeneID 5241) and HER-2 markers (v-erb-b2erythroblastic leukemia viral oncogene homolog 2, Entrez GeneID 2064).Recurrence data from TLE3-positive and TLE3-negative patients were usedto generate the top and bottom curves, respectively. As shown in theFigure, antibody binding to the TLE3 marker correlates with improvedprognosis across this breast cancer cohort (HR=0.24, p<0.011).

FIG. 4 shows Kaplan-Meier recurrence curves that were generated usingpatients in the HH breast cancer cohort of FIG. 1 that did not receivechemotherapy. Recurrence data from TLE3-positive and TLE3-negativepatients in this subset were used to generate the top and bottom curves,respectively. As shown in the Figure, antibody binding to the TLE3marker loses its correlation with prognosis in breast cancer patientsthat did not receive chemotherapy (HR=0.788, p=0.49).

FIG. 5 shows Kaplan-Meier recurrence curves that were generated usingpatients in the HH breast cancer cohort of FIG. 1 that did receivechemotherapy. Recurrence data from TLE3-positive and TLE3-negativepatients in this subset were used to generate the top and bottom curves,respectively. As shown in the Figure, the correlation between antibodybinding to the TLE3 marker and prognosis was restored in patients thatdid receive chemotherapy (HR=0.539, p<0.013).

FIG. 6 shows Kaplan-Meier recurrence curves that were generated usingpatients in the RP breast cancer cohort of FIG. 2 that did receivechemotherapy. Recurrence data from TLE3-positive and TLE3-negativepatients in this subset were used to generate the top and bottom curves,respectively. As shown in the Figure, antibody binding to the TLE3marker correlates with improved prognosis across this subset of breastcancer patients (HR=0.194, p=0.010). These results parallel thoseobtained in FIG. 5 with the HH cohort.

FIG. 7 shows Kaplan-Meier recurrence curves that were generated usingpatients in the HH breast cancer cohort of FIG. 5 that received CMF(cyclophosphamide, methotrexate and 5-fluorouracil) chemotherapy.Recurrence data from TLE3-positive and TLE3-negative patients in thissubset were used to generate the top and bottom curves, respectively. Asshown in the Figure, antibody binding to the TLE3 marker correlates withimproved prognosis across this subset of treated patients (HR=0.398,p<0.019).

FIG. 8 shows Kaplan-Meier recurrence curves that were generated usingpatients in the HH breast cancer cohort of FIG. 5 that received CA(cyclophosphamide and adriamycin) or CAF (cyclophosphamide, adriamycinand 5-fluorouracil) chemotherapy (with or without a taxane). Recurrencedata from TLE3-positive and TLE3-negative patients in this subset wereused to generate the top and bottom curves, respectively. As shown inthe Figure, the correlation between antibody binding to the TLE3 markerand prognosis loses significance in this subset of treated patients(HR=0.666, p=0.22).

FIG. 9 shows Kaplan-Meier recurrence curves that were generated usingpatients in the HH breast cancer cohort of FIG. 8 that received CA orCAF chemotherapy only (i.e., without a taxane). Recurrence data fromTLE3-positive and TLE3-negative patients in this subset were used togenerate the top and bottom curves, respectively. As shown in theFigure, there is no correlation between antibody binding to the TLE3marker and prognosis in this subset of treated patients (HR=1.03,p=0.95).

FIG. 10 shows Kaplan-Meier recurrence curves that were generated usingpatients in the HH breast cancer cohort of FIG. 8 that received CA orCAF in combination with a taxane. Recurrence data from TLE3-positive andTLE3-negative patients in this subset were used to generate the top andbottom curves, respectively. As shown in the Figure, the correlationbetween antibody binding to the TLE3 marker and prognosis was restoredin this subset of treated patients (HR=0.114, p=0.038).

FIG. 11 shows Kaplan-Meier recurrence curves that were generated usingpatients in the RP breast cancer cohort of FIG. 6 that received CAchemotherapy only (i.e., without a taxane). Recurrence data fromTLE3-positive and TLE3-negative patients in this subset were used togenerate the top and bottom curves, respectively. As shown in theFigure, there is no correlation between antibody binding to the TLE3marker and prognosis in this subset of treated patients (HR=0.759,p=0.81).

FIG. 12 shows Kaplan-Meier recurrence curves that were generated usingpatients in the RP breast cancer cohort of FIG. 6 that received CA incombination with a taxane. Recurrence data from TLE3-positive andTLE3-negative patients in this subset were used to generate the top andbottom curves, respectively. As shown in the Figure, antibody binding tothe TLE3 marker correlates with improved prognosis across this subset oftreated patients (HR=0.142, p=0.011).

FIG. 13 shows Kaplan-Meier recurrence curves that were generated usingpatients in the RP breast cancer cohort of FIG. 6 that received a taxaneor CMF. Some of the patients receiving a taxane also received CA.Recurrence data from TLE3-positive and TLE3-negative patients in thissubset were used to generate the top and bottom curves, respectively. Asshown in the Figure, antibody binding to the TLE3 marker correlates withimproved prognosis across this subset of treated patients (HR=0.137,p=0.011).

FIG. 14 shows Kaplan-Meier recurrence curves that were generated usingpatients in the RP breast cancer cohort of FIG. 6 that receivedneoadjuvant chemotherapy. Recurrence data from TLE3-positive andTLE3-negative patients in this subset were used to generate the top andbottom curves, respectively. The sample size was small (N=12); however,as shown in the Figure, antibody binding to the TLE3 marker showedsignificant correlation with improved prognosis across this subset oftreated patients when measured using the Fisher Exact Test (p=0.005).

FIGS. 15-17 show Kaplan-Meier recurrence curves that were generatedusing patients in the RP breast cancer cohort of FIG. 6 that receivedchemotherapy. Recurrence data from TLE3-positive and TLE3-negativepatients with stage II+ (FIG. 15), stage IIb+ (FIG. 16) and stage III+(FIG. 17) cancers were used to generate the top and bottom curves,respectively. In each case, antibody binding to the TLE3 markercorrelated with improved prognosis across these subsets of treatedpatients. The sample size was small in the subset of FIG. 17 (N=19);however significance was obtained when measured using the Fisher ExactTest (p=0.020).

FIG. 18 shows Kaplan-Meier recurrence curves that were generated usingpatients in the University of Alabama at Birmingham (UAB) ovarian cancercohort. All patients received paclitaxel. Most patients also receivedplatinum chemotherapy (carboplatin or cisplatin). Recurrence data fromTLE3-positive and TLE3-negative patients in this subset were used togenerate the top and bottom curves, respectively. As shown in theFigure, antibody binding to the TLE3 marker correlated with prognosis inthese treated patients (HR=0.64, p<0.049).

DEFINITIONS

Binds—When an interaction partner “binds” a marker they are linked bydirect non-covalent interactions.

Cancer markers—“Cancer markers” or “markers” are molecular entities thatare detectable in cancer samples. Generally, markers may be polypeptides(e.g., TLE3 protein) or polynucleotides (e.g., TLE3 mRNA) that areindicative of the expression of a gene (e.g., TLE3 gene) and presentwithin the cancer sample, e.g., within the cytoplasm or membranes ofcancerous cells and/or secreted from such cells.

Cancer sample—As used herein, the term “cancer sample” or “sample” istaken broadly to include cell or tissue samples removed from a cancerpatient (e.g., from a tumor, from the bloodstream, etc.), cells derivedfrom a tumor that may be located elsewhere in the body (e.g., cells inthe bloodstream or at a site of metastasis), or any material derivedfrom such a sample. Derived material may include, for example, nucleicacids or proteins extracted from the sample, cell progeny, etc. In oneembodiment, a cancer sample may be a tumor sample.

Correlation—“Correlation” refers to the degree to which one variable canbe predicted from another variable, e.g., the degree to which a cancer'sresponse to therapy can be predicted from the expression of a marker ina cancer sample. A variety of statistical methods may be used to measurecorrelation between two variables, e.g., without limitation the studentt-test, the Fisher exact test, the Pearson correlation coefficient, theSpearman correlation coefficient, the Chi squared test, etc. Results aretraditionally given as a measured correlation coefficient with a p-valuethat provides a measure of the likelihood that the correlation arose bychance. A correlation with a p-value that is less than 0.05 is generallyconsidered to be statistically significant. Preferred correlations havep-values that are less than 0.01, especially less than 0.001.

Hybridized—When a primer and a marker are physically “hybridized” withone another as described herein, they are non-covalently linked by basepair interactions.

Interaction partner—An “interaction partner” is an entity that binds apolypeptide marker. For example and without limitation, an interactionpartner may be an antibody or a fragment thereof that binds a marker. Ingeneral, an interaction partner is said to “bind specifically” with amarker if it binds at a detectable level with the marker and does notbind detectably with unrelated molecular entities (e.g., other markers)under similar conditions. Specific association between a marker and aninteraction partner will typically be dependent upon the presence of aparticular structural feature of the target marker such as an antigenicdeterminant or epitope recognized by the interaction partner. Ingeneral, it is to be understood that specificity need not be absolute.For example, it is well known in the art that antibodies frequentlycross-react with other epitopes in addition to the target epitope. Suchcross-reactivity may be acceptable depending upon the application forwhich the interaction partner is to be used. Thus the degree ofspecificity of an interaction partner will depend on the context inwhich it is being used. In general, an interaction partner exhibitsspecificity for a particular marker if it favors binding with thatpartner above binding with other potential partners, e.g., othermarkers. One of ordinary skill in the art will be able to selectinteraction partners having a sufficient degree of specificity toperform appropriately in any given application (e.g., for detection of atarget marker, for therapeutic purposes, etc.). It is also to beunderstood that specificity may be evaluated in the context ofadditional factors such as the affinity of the interaction partner forthe target marker versus the affinity of the interaction partner forother potential partners, e.g., other markers. If an interaction partnerexhibits a high affinity for a target marker and low affinity fornon-target molecules, the interaction partner will likely be anacceptable reagent for diagnostic purposes even if it lacks specificity.

Primer—A “primer” is an oligonucleotide entity that physicallyhybridizes with a polynucleotide marker. In general, a primer is said to“hybridize specifically” with a marker if it hybridizes at a detectablelevel with the marker and does not hybridize detectably with unrelatedmolecular entities (e.g., other markers) under similar conditions.Specific hybridization between a marker and a primer will typically bedependent upon the presence of a particular nucleotide sequence of thetarget marker which is complementary to the nucleotide sequence of theprimer. In general, it is to be understood that specificity need not beabsolute. The degree of specificity of a primer will depend on thecontext in which it is being used. In general, a primer exhibitsspecificity for a particular marker if it favors hybridization with thatpartner above hybridization with other potential partners, e.g., othermarkers. One of ordinary skill in the art will be able to select primershaving a sufficient degree of specificity to perform appropriately inany given application. It is also to be understood that specificity maybe evaluated in the context of additional factors such as the affinityof the primer for the target marker versus the affinity of the primerfor other potential partners, e.g., other markers. If a primer exhibitsa high affinity for a target marker and low affinity for non-targetmolecules, the primer will likely be an acceptable reagent fordiagnostic purposes even if it lacks specificity.

Response—The “response” of a cancer to therapy may represent anydetectable change, for example at the molecular, cellular, organellar,or organismal level. For instance, tumor size, patient life expectancy,recurrence, or the length of time the patient survives, etc., are allresponses. Responses can be measured in any of a variety of ways,including for example non-invasive measuring of tumor size (e.g., CTscan, image-enhanced visualization, etc.), invasive measuring of tumorsize (e.g., residual tumor resection, etc.), surrogate markermeasurement (e.g., serum PSA, etc.), clinical course variance (e.g.,measurement of patient quality of life, time to relapse, survival time,etc.).

Small molecule—A “small molecule” is a non-polymeric molecule. A smallmolecule can be synthesized in a laboratory (e.g., by combinatorialsynthesis) or found in nature (e.g., a natural product). A smallmolecule is typically characterized in that it contains severalcarbon-carbon bonds and has a molecular weight of less than about 1500Da, although this characterization is not intended to be limiting forthe purposes of the present invention.

DETAILED DESCRIPTION OF CERTAIN PREFERRED EMBODIMENTS OF THE INVENTION

As noted above, we have identified a correlation between the expressionof TLE3 (transducin-like enhancer of split 3, Entrez Gene ID 7090) in acancer sample and a cancer's response to chemotherapy. As described inthe Examples, this correlation has been demonstrated using TLE3antibodies and samples from two breast cancer cohorts which include bothtreated and untreated patients with known outcome. We have also shownthat this predictive model is consistent when applied to samples from acohort of treated ovarian cancer patients. We have also demonstrated theutility of TLE3 for predicting response to specific types ofchemotherapies including treatments which involve the administration ofcell cycle specific chemotherapeutics, e.g., methotrexate and taxanes.Since these chemotherapeutics have known utility across different cancertypes, these results suggest that the inventive methods will also beuseful in predicting their efficacy across different cancer types.

Predicting Response to Chemotherapy and Selecting Chemotherapy

In one aspect, the present invention provides methods of using TLE3 as amarker for predicting the likelihood that a patient's cancer willrespond to chemotherapy. In general, these methods involve providing acancer sample from a cancer patient, determining whether TLE3 isexpressed in the cancer sample, and predicting the likelihood that thepatient's cancer will respond to chemotherapy based upon a result of thestep of determining. In one embodiment, the step of predicting comprisespredicting that the patient's cancer is likely to respond tochemotherapy based upon the presence of TLE3 expression in the cancersample. In one embodiment, the step of predicting comprises predictingthat the patient's cancer is unlikely to respond to chemotherapy basedupon the absence of TLE3 expression in the cancer sample.

In certain embodiments, a negative control sample is provided and thestep of determining comprises detecting a level of TLE3 expression inthe cancer sample and the negative control sample and comparing thelevel of expression of TLE3 in the cancer sample and the negativecontrol sample. In general, the negative control sample can be anysample that does not reproducibly express TLE3. In one embodiment, thenegative control sample can be a sample that does not reproducibly bindTLE3 antibodies. In one embodiment, the negative control sample can be asample that does not reproducibly produce a detectable level of TLE3mRNA. In one embodiment, the negative control sample can be from apatient with a TLE3-negative cancer. In one embodiment, the negativecontrol sample can be from a patient without cancer. In certainembodiments the negative control sample may originate from the sametissue type as the cancer in question (e.g., breast tissue whenconsidering breast cancer). In other embodiments, the negative controlsample may originate from a different tissue type or even a differentorganism, or a cell line.

Additionally or alternatively, in certain embodiments, a positivecontrol sample is provided and the step of determining comprisesdetecting a level of TLE3 expression in the cancer sample and thepositive control sample and comparing the level of expression of TLE3 inthe cancer sample and the positive control sample. In general, thepositive control sample can be any sample that reproducibly expressesTLE3. In one embodiment, the negative control sample can be a samplethat reproducibly bind TLE3 antibodies. In one embodiment, the negativecontrol sample can be a sample that reproducibly produces a detectablelevel of TLE3 mRNA. In one embodiment, the positive control sample canbe from a patient with a TLE3-positive cancer. In certain embodimentsthe positive control sample may originate from the same tissue type asthe cancer in question (e.g., breast tissue when considering breastcancer). In other embodiments, the positive control sample may originatefrom a different tissue type or even a different organism, or cell line.

Expression of TLE3 can be determined using any known method.

In one embodiment, TLE3 polypeptides may be detected using aninteraction partner that binds a TLE3 polypeptide (e.g., TLE3 protein oran antigenic fragment thereof). For example, as described below one mayuse a TLE3 antibody as an interaction partner and detect TLE3 expressionby contacting the cancer sample with the TLE3 antibody. In suchembodiments, the inventive methods may involve providing a cancer samplefrom a cancer patient, contacting the cancer sample with an antibodydirected to TLE3, and predicting the likelihood that the patient'scancer will respond to chemotherapy based upon binding of the antibodyto the cancer sample. In one embodiment, the step of predicting maycomprise predicting that the patient's cancer is likely to respond tochemotherapy based upon binding of the antibody to the cancer sample. Inanother embodiment, the step of predicting may comprise predicting thatthe patient's cancer is unlikely to respond to chemotherapy based uponlack of binding of the antibody to the cancer sample.

In another embodiment, TLE3 polynucleotides may be detected using one ormore primers that hybridize with a TLE3 polynucleotide (e.g., a TLE3mRNA, cDNA or RNA). In such embodiments, the inventive methods mayinvolve providing a cancer sample from a cancer patient, contacting thecancer sample with one or more primers that hybridize with TLE3, andpredicting the likelihood that the patient's cancer will respond tochemotherapy based upon hybridization of the one or more primers to thecancer sample. In one embodiment, the step of predicting may comprisepredicting that the patient's cancer is likely to respond tochemotherapy based upon hybridization of the one or more primers to thecancer sample. In another embodiment, the step of predicting maycomprise predicting that the patient's cancer is unlikely to respond tochemotherapy based upon lack of hybridization of the one or more primersto the cancer sample.

In another aspect, the present invention provides methods for decidingwhether to administer chemotherapy to the cancer patient based upon thelikelihood that the patient's cancer will respond to chemotherapy. Inone embodiment, the step of deciding comprises deciding to administerchemotherapy to the cancer patient based upon the presence of TLE3expression in the cancer sample. In one embodiment, the step of decidingcomprises deciding not to administer chemotherapy to the cancer patientbased upon the absence of TLE3 expression in the cancer sample.

In yet another aspect, the present invention provides methods forselecting a chemotherapy for a cancer patient. In general, these methodscomprise providing a cancer sample from a cancer patient, determiningwhether TLE3 is expressed in the cancer sample, and selecting achemotherapy for the cancer patient based upon the results of the stepof determining. In one embodiment, the step of selecting comprisesselecting a chemotherapy based upon the presence of TLE3 expression inthe cancer sample.

As described in the Examples, we have demonstrated that TLE3 expressioncorrelates with response to chemotherapy with methotrexate (see FIG. 7)and taxanes (see FIGS. 10, 12 and 13). Methotrexate and taxanes arethought to be cell cycle specific chemotherapeutics (e.g., see Goodman &Gilman's The Pharmacological Basis of Therapeutics, IX. Chemotherapy ofNeoplastic Diseases Chapter 51. Antineoplastic Agents, 1 lth Edition,Laurence L. Brunton, editor-in-chief, John S. Lazo and Keith L. Parker,Associate Editors). Cell cycle specific chemotherapeutics exhibit theirmechanism of action within a specific phase of the cell cycle incontrast to non-cell cycle specific chemotherapeutics that work equallywith all phases including the resting phase (GO). Other plant alkaloidsbesides the taxanes have also been classified in the literature as cellcycle specific chemotherapeutics as have other antimetabolites besidesmethotrexate. In contrast, many alkylating agents such as cisplatin andcyclophosamide have been classified as non-cell cycle specificchemotherapeutics. Our results suggest that the predictive power of TLE3may extend to other cell cycle specific chemotherapeutics besidesmethotrexate and taxanes.

In some embodiments, the inventive methods may therefore be used toselect, or decide whether to administer, a cell cycle specificchemotherapeutic. In one embodiment, the inventive methods may be usedto select, or decide whether to administer, an antimetabolite. In oneembodiment, the inventive methods may be used to select, or decidewhether to administer, a plant alkaloid. In one embodiment, theinventive methods may be used to select, or decide whether toadminister, methotrexate. In another embodiment, the inventive methodsmay be used to select, or decide whether to administer, a taxane. In oneembodiment the taxane is paclitaxel. In one embodiment the taxane isdocetaxel.

In each case it will be appreciated that these chemotherapeutics may beadministered alone or in combination with other chemotherapeutics as isknown in the art and discussed below. It will also be appreciated thatthe present invention encompasses methods in which the selectedchemotherapeutic is a methotrexate or taxane derivative, i.e., acompound with a structure which is derived from methotrexate or ataxane. Derivatives will typically share most of the structure of theparent compound but may include different substituents, heteroatoms,ring fusions, levels of saturation, isomerism, stereoisomerism, etc. atone or more positions within the parent compound. Without limitation,the following U.S. patents describe the preparation of exemplarymethotrexate derivatives that could be employed according to aninventive method: U.S. Pat. Nos. 6,559,149 and 4,374,987. Withoutlimitation, the following U.S. patents describe the preparation ofexemplary taxane derivatives that could be employed according to aninventive method: U.S. Pat. Nos. 7,074,945; 7,063,977; 6,906,101;6,649,778; 6,596,880; 6,552,205; 6,531,611; 6,482,963; 6,482,850;6,462,208; 6,455,575; 6,441,026; 6,433,180; 6,392,063; 6,369,244;6,339,164; 6,291,690; 6,268,381; 6,239,167; 6,218,553; 6,214,863;6,201,140; 6,191,290; 6,187,916; 6,162,920; 6,147,234; 6,136,808;6,114,550; 6,107,332; 6,051,600; 6,025,385; 6,011,056; 5,955,489;5,939,567; 5,912,263; 5,908,835; 5,869,680; 5,861,515; 5,821,263;5,763,477; 5,750,561; 5,728,687; 5,726,346; 5,726,318; 5,721,268;5,719,177; 5,714,513; 5,714,512; 5,703,117; 5,698,582; 5,686,623;5,677,462; 5,646,176; 5,637,723; 5,621,121; 5,616,739; 5,606,083;5,580,899; 5,476,954; 5,403,858; 5,380,916; 5,254,703; and 5,250,722.The entire contents of each of the aforementioned patents and any otherreference which is cited herein is hereby incorporated by reference.

Methotrexate acts by inhibiting the metabolism of folic acid and hasbeen approved for the treatment of bladder cancer, breast cancer,gastric cancer, choriocarcinoma, head and neck cancer, leptomeningealcancer, leukemia (acute meningeal, acute lymphoblastic, acutelymphocytic), lymphoma (Burkitt's, childhood, non-Hodgkin's), mycosisfungoides, primary unknown cancer and lymphatic sarcoma (Methotrexate inBC Cancer Agency Cancer Drug Manual, 2007). Methotrexate has also beenshown to be useful for treating esophageal cancer, lung cancer andtesticular cancer (Methotrexate in UpToDate, 2007). In certainembodiments, the inventive methods comprise a step of selecting, ordeciding whether to administer, methotrexate in combination with one ormore additional chemotherapeutics. For example, methotrexate is commonlyadministered to cancer patients as a combination called CMF which alsoincludes cyclophosphamide and 5-fluorouracil.

Taxanes are diterpenes produced by the plants of the genus Taxus.Taxanes can be obtained from natural sources or produced synthetically.Taxanes include paclitaxel (TAXOL™) and docetaxel (TAXOTERE™). Taxaneswork by interfering with normal microtubule growth during cell division.In certain embodiments, the inventive methods comprise a step ofselecting, or deciding whether to administer, a taxane (e.g., paclitaxelor docetaxel) in combination with one or more additionalchemotherapeutics. For example, taxanes are commonly administered tocancer patients in combination with cyclophosphamide and adriamycin(doxorubicin) and optionally 5-fluorouracil (i.e., with CA or CAF).

Paclitaxel has been approved for the treatment of breast cancer,Kaposi's sarcoma, lung cancer and ovarian cancer (Paclitaxel in BCCancer Agency Cancer Drug Manual, 2007 and Mekhail and Markman, ExpertOpin. Pharmacother. 3:755-66, 2002). Paclitaxel has also been shown tobe useful in treating cervical cancer (pp. 1124-34 in AHFS 2005 DrugInformation. Bethesda, Md.: American Society of Health-SystemPharmacists, 2005), endometrial cancer (Paclitaxel in BC Cancer AgencyCancer Drug Manual, 2007), bladder cancer (Paclitaxel in UpToDate,2007), head and neck cancer (Paclitaxel in UpToDate, 2007), leukemia(Paclitaxel in UpToDate, 2007) and malignant melanoma (Paclitaxel inUpToDate, 2007). Side effects of paclitaxel include hypersensitivityreactions such as flushing of the face, skin rash, or shortness ofbreath. Patients often receive medication to prevent hypersensitivityreactions before they take paclitaxel. Paclitaxel can also causetemporary damage to the bone marrow. Bone marrow damage can cause aperson to be more susceptible to infection, anemia, and bruise or bleedeasily. Other side effects may include joint or muscle pain in the armsor legs; diarrhea; nausea and vomiting; numbness, burning, or tinglingin the hands or feet; and loss of hair.

Docetaxel has been approved for the treatment of breast cancer (Aapro,Seminars in Oncology 25(5 Suppl 12):7-11, 1998; Nabholtz et al., Journalof Clinical Oncology 17(5):1413-24, 1999; Sjostrom et al., EuropeanJournal of Cancer 35(8):1194-201, 1999; and Burstein et al., Journal ofClinical Oncology 18(6):1212-9, 2000), non-small cell lung cancer(Fossella et al., Journal of Clinical Oncology 18(12):2354-62, 2000 andHainsworth et al., Cancer 89(2):328-33, 2000) and ovarian cancer (Kayeet al., European Journal of Cancer 33(13):2167-70, 1997). Docetaxel hasalso been shown to be useful in treating esothelioma (Vorobiof et al.,Proc Am Soc Clin Oncol 19:578a, 2000), prostate cancer (Picus et al.,Seminars in Oncology 26(5 Suppl 17):14-8, 1999 and Petrylak et al.,Journal of Clinical Oncology 17(3):958-67, 1999), urothelialtransitional cell cancer (Dimopoulos et al., Annals of Oncology10(11):1385-8, 1999 and Pectasides et al., European Journal of Cancer36(1):74-9, 2000), head and neck cancer (Docetaxel in USP DI, 2000 andCouteau et al., British Journal of Cancer 81(3):457-62, 1999) and smallcell lung cancer (Smyth et al., European Journal of Cancer30A(8):1058-60, 1994).

Our observation that improved response to chemotherapy is observed forboth breast and ovarian cancer patients that are TLE3-positive suggeststhat the inventive methods may be useful across different cancer types.Our observation that TLE3 expression is associated with improvedresponse to treatment with methotrexate and taxanes further suggest thatthe inventive methods may be applicable across cancers that respond tothese chemotherapeutics. As discussed above, this includes withoutlimitation breast cancer, ovarian cancer, lung cancer, bladder cancer,gastric cancer, head and neck cancer, and leukemia.

In one embodiment, the inventive methods may be used with a cancerpatient that has breast cancer. In one embodiment, the inventive methodsmay be used with a cancer patient that has ovarian cancer. In oneembodiment, the inventive methods may be used with a cancer patient thathas lung cancer. In one embodiment, the inventive methods may be usedwith a cancer patient that has bladder cancer. In one embodiment, theinventive methods may be used with a cancer patient that has gastriccancer. In one embodiment, the inventive methods may be used with acancer patient that has head and neck cancer. In one embodiment, theinventive methods may be used with a cancer patient that has leukemia.

As demonstrated in the Examples, in one embodiment, the correlationbetween TLE3 expression and response to chemotherapy was observed withbreast cancer patients that are triple negative for the ER (estrogenreceptor, Entrez GeneID 2099), PR (progesterone receptor, Entrez GeneID5241) and HER-2 markers (v-erb-b2 erythroblastic leukemia viral oncogenehomolog 2, Entrez GeneID 2064). In certain embodiments, the inventivemethods may therefore be used with breast cancer patients that belong tothis class.

As demonstrated in the Examples, the correlation between TLE3 expressionand response to chemotherapy was found to also exist when treatment wasadministered in a neoadjuvant setting. Thus, in certain embodiments, theinventive methods may be used with patients receiving chemotherapy in aneoadjuvant setting. In other embodiments, the chemotherapy may beadministered in an adjuvant setting.

As demonstrated in the Examples, the correlation between TLE3 expressionand response to chemotherapy was also found to be independent of stage.Thus, in certain embodiments, the inventive methods may be used withpatients with a stage II+ (i.e., stage II or greater) cancer. In certainembodiments, the inventive methods may be used with patients with astage IIb+ or a stage III+ cancer.

Detecting TLE3 Expression

As mentioned above, expression of TLE3 can be determined using any knownmethod. In one embodiment, TLE3 expression may be determined bydetecting TLE3 polypeptide markers using interaction partners (e.g.,antibodies). In another embodiment, TLE3 expression may be determined bydetecting TLE3 polynucleotide markers using primers.

Detecting TLE3 Polypeptide Markers

TLE3 polypeptide markers may be detected using any interaction partnerthat binds a TLE3 polypeptide marker (which could be a TLE3 protein oran antigenic fragment thereof). Thus, any entity that binds detectablyto the TLE3 marker may be utilized as an interaction partner inaccordance with the present invention, so long as it binds the markerwith an appropriate combination of affinity and specificity.

Particularly preferred interaction partners are antibodies, or fragments(e.g., F(ab) fragments, F(ab′)₂ fragments, Fv fragments, or sFvfragments, etc.; see, for example, Inbar et al., Proc. Nat. Acad. Sci.USA 69:2659, 1972; Hochman et al., Biochem. 15:2706, 1976; and Ehrlichet al., Biochem. 19:4091, 1980; Huston et al., Proc. Nat. Acad. Sci. USA85:5879, 1998; U.S. Pat. Nos. 5,091,513 and 5,132,405 to Huston et al.;and U.S. Pat. No. 4,946,778 to Ladner et al., each of which isincorporated herein by reference). In certain embodiments, interactionpartners may be selected from libraries of mutant antibodies (orfragments thereof). For example, collections of antibodies that eachinclude different point mutations may be screened for their associationwith a marker of interest. Yet further, chimeric antibodies may be usedas interaction partners, e.g., “humanized” or “veneered” antibodies asdescribed in greater detail below.

When antibodies are used as interaction partners, these may be preparedby any of a variety of techniques known to those of ordinary skill inthe art (e.g., see Harlow and Lane, Antibodies: A Laboratory Manual,Cold Spring Harbor Laboratory, 1988, see also the Examples). Forexample, antibodies can be produced by cell culture techniques,including the generation of monoclonal antibodies, or via transfectionof antibody genes into suitable bacterial or mammalian cell hosts, inorder to allow for the production of recombinant antibodies. In onetechnique, an “immunogen” comprising an antigenic portion of a marker ofinterest (or the marker itself) is initially injected into any of a widevariety of mammals (e.g., mice, rats, rabbits, sheep or goats). In thisstep, a marker (or an antigenic portion thereof) may serve as theimmunogen without modification. Alternatively, particularly forrelatively short markers, a superior immune response may be elicited ifthe marker is joined to a carrier protein, such as bovine serum albuminor keyhole limpet hemocyanin (KLH). The immunogen is injected into theanimal host, preferably according to a predetermined scheduleincorporating one or more booster immunizations and the animals are bledperiodically. Polyclonal antibodies specific for the marker may then bepurified from such antisera by, for example, affinity chromatographyusing the marker (or an antigenic portion thereof) coupled to a suitablesolid support. An exemplary method is described in the Examples.

If desired for diagnostic or therapeutic purposes, monoclonal antibodiesspecific for TLE3 may be prepared, for example, using the technique ofKohler and Milstein, Eur. J. Immunol. 6:511, 1976 and improvementsthereto. Briefly, these methods involve the preparation of immortal celllines capable of producing antibodies having the desired specificity(i.e., reactivity with the marker of interest). Such cell lines may beproduced, for example, from spleen cells obtained from an animalimmunized as described above. The spleen cells are then immortalized by,for example, fusion with a myeloma cell fusion partner, preferably onethat is syngeneic with the immunized animal. A variety of fusiontechniques may be employed. For example, the spleen cells and myelomacells may be combined with a nonionic detergent for a few minutes andthen plated at low density on a selective medium that supports thegrowth of hybrid cells, but not myeloma cells. A preferred selectiontechnique uses HAT (hypoxanthine, aminopterin, thymidine) selection.After a sufficient time, usually about 1 to 2 weeks, colonies of hybridsare observed. Single colonies are selected and their culturesupernatants tested for binding activity against the marker. Hybridomashaving high reactivity and specificity are preferred.

Monoclonal antibodies may be isolated from the supernatants of growinghybridoma colonies. In addition, various techniques may be employed toenhance the yield, such as injection of the hybridoma cell line into theperitoneal cavity of a suitable vertebrate host, such as a mouse.Monoclonal antibodies may then be harvested from the ascites fluid orthe blood. Contaminants may be removed from the antibodies byconventional techniques, such as chromatography, gel filtration,precipitation and extraction. TLE3 may be used in the purificationprocess in, for example, an affinity chromatography step.

It is to be understood that the present invention is not limited tousing antibodies or antibody fragments as interaction partners. Inparticular, the present invention also encompasses the use of syntheticinteraction partners that mimic the functions of antibodies. Severalapproaches to designing and/or identifying antibody mimics have beenproposed and demonstrated (e.g., see the reviews by Hsieh-Wilson et al.,Acc. Chem. Res. 29:164, 2000 and Peczuh and Hamilton, Chem. Rev.100:2479, 2000). For example, small molecules that bind protein surfacesin a fashion similar to that of natural proteins have been identified byscreening synthetic libraries of small molecules or natural productisolates (e.g., see Gallop et al., J. Med. Chem. 37:1233, 1994; Gordonet al., J. Med. Chem. 37:1385, 1994; DeWitt et al., Proc. Natl. Acad.Sci. U.S.A. 90:6909, 1993; Bunin et al., Proc. Natl. Acad. Sci. U.S.A.91:4708, 1994; Virgilio and Ellman, J. Am. Chem. Soc. 116:11580, 1994;Wang et al., J. Med. Chem. 38:2995, 1995; and Kick and Ellman, J. Med.Chem. 38:1427, 1995). Similarly, combinatorial approaches have beensuccessfully applied to screen libraries of peptides and proteins fortheir ability to bind a range of proteins (e.g., see Cull et al., Proc.Natl. Acad. Sci. U.S.A. 89:1865, 1992; Mattheakis et al., Proc. Natl.Acad. Sci. U.S.A. 91:9022, 1994; Scott and Smith, Science 249:386, 1990;Devlin et al., Science 249:404, 1990; Corey et al., Gene 128:129, 1993;Bray et al., Tetrahedron Lett. 31:5811, 1990; Fodor et al., Science251:767, 1991; Houghten et al., Nature 354:84, 1991; Lam et al., Nature354:82, 1991; Blake and Litzi-Davis, Bioconjugate Chem. 3:510, 1992;Needels et al., Proc. Natl. Acad. Sci. U.S.A. 90:10700, 1993; andOhlmeyer et al., Proc. Natl. Acad. Sci. U.S.A. 90:10922, 1993). Similarapproaches have also been used to study carbohydrate-proteininteractions (e.g., see Oldenburg et al., Proc. Natl. Acad. Sci. U.S.A.89:5393, 1992) and polynucleotide-protein interactions (e.g., seeEllington and Szostak, Nature 346:818, 1990 and Tuerk and Gold, Science249:505, 1990). These approaches have also been extended to studyinteractions between proteins and unnatural biopolymers such asoligocarbamates, oligoureas, oligosulfones, etc. (e.g., see Zuckermannet al., J. Am. Chem. Soc. 114:10646, 1992; Simon et al., Proc. Natl.Acad. Sci. U.S.A. 89:9367, 1992; Zuckermann et al., J. Med. Chem.37:2678, 1994; Burgess et al., Angew. Chem., Int. Ed. Engl. 34:907,1995; and Cho et al., Science 261:1303, 1993). Yet further, alternativeprotein scaffolds that are loosely based around the basic fold ofantibody molecules have been suggested and may be used in thepreparation of inventive interaction partners (e.g., see Ku and SchultzProc. Natl. Acad. Sci. U.S.A. 92:6552, 1995). Antibody mimics comprisinga scaffold of a small molecule such as 3-aminomethylbenzoic acid and asubstituent consisting of a single peptide loop have also beenconstructed. The peptide loop performs the binding function in thesemimics (e.g., see Smythe et al., J. Am. Chem. Soc. 116:2725, 1994). Asynthetic antibody mimic comprising multiple peptide loops built arounda calixarene unit has also been described (e.g., see U.S. Pat. No.5,770,380 to Hamilton et al.).

Any available strategy or system may be utilized to detect associationbetween an interaction partner and the TLE3 marker. In certainembodiments, association can be detected by adding a detectable label tothe interaction partner. In other embodiments, association can bedetected by using a labeled secondary interaction partner that bindsspecifically with the primary interaction partner, e.g., as is wellknown in the art of antigen/antibody detection. The detectable label maybe directly detectable or indirectly detectable, e.g., through combinedaction with one or more additional members of a signal producing system.Examples of directly detectable labels include radioactive,paramagnetic, fluorescent, light scattering, absorptive and colorimetriclabels. Examples of indirectly detectable include chemiluminescentlabels, e.g., enzymes that are capable of converting a substrate to achromogenic product such as alkaline phosphatase, horseradish peroxidaseand the like.

Once a labeled interaction partner has bound the TLE3 marker, thecomplex may be visualized or detected in a variety of ways, with theparticular manner of detection being chosen based on the particulardetectable label, where representative detection means include, e.g.,scintillation counting, autoradiography, measurement of paramagnetism,fluorescence measurement, light absorption measurement, measurement oflight scattering and the like.

In general, association between an interaction partner and the TLE3marker may be assayed by contacting the interaction partner with acancer sample that includes the marker. Depending upon the nature of thesample, appropriate methods include, but are not limited to,immunohistochemistry (IHC), radioimmunoassay, ELISA, immunoblotting andfluorescence activates cell sorting (FACS). In the case where theprotein is to be detected in a tissue sample, e.g., a biopsy sample, IHCis a particularly appropriate detection method. Techniques for obtainingtissue and cell samples and performing IHC and FACS are well known inthe art.

Where large numbers of samples are to be handled (e.g., whensimultaneously analyzing several samples from the same patient orsamples from different patients), it may be desirable to utilize arrayedand/or automated formats. In certain embodiments, tissue arrays asdescribed in the Examples may be used. Tissue arrays may be constructedaccording to a variety of techniques. According to one procedure, acommercially-available mechanical device (e.g., the manual tissuearrayer MTA1 from Beecher Instruments of Sun Prairie, Wis.) is used toremove an 0.6-micron-diameter, full thickness “core” from a paraffinblock (the donor block) prepared from each patient, and to insert thecore into a separate paraffin block (the recipient block) in adesignated location on a grid. In preferred embodiments, cores from asmany as about 400 patients (or multiple cores from the same patient) canbe inserted into a single recipient block; preferably, core-to-corespacing is approximately 1 mm. The resulting tissue array may beprocessed into thin sections for staining with interaction partnersaccording to standard methods applicable to paraffin embedded material.

Whatever the format, and whatever the detection strategy, identificationof a discriminating titer can simplify binding studies to assess thedesirability of using an interaction partner. In such studies, theinteraction partner is contacted with a plurality of different samplesthat preferably have at least one common trait (e.g., tissue of origin),and often have multiple common traits (e.g., tissue of origin, stage,microscopic characteristics, etc.). In some cases, it will be desirableto select a group of samples with at least one common trait and at leastone different trait, so that a titer is determined that distinguishesthe different trait. In other cases, it will be desirable to select agroup of samples with no detectable different traits, so that a titer isdetermined that distinguishes among previously indistinguishablesamples. Those of ordinary skill in the art will understand, however,that the present invention often will allow both of these goals to beaccomplished even in studies of sample collections with varying degreesof similarity and difference.

As discussed above and in the Examples, the inventors have applied thesetechniques to samples from breast and ovarian cancer patients. Theinvention also encompasses the recognition that markers that aresecreted from the cells in which they are produced may be present inserum, enabling their detection through a blood test rather thanrequiring a biopsy specimen. An interaction partner that binds to suchmarkers represents a particularly preferred embodiment of the invention.

In general, the results of such an assay can be presented in any of avariety of formats. The results can be presented in a qualitativefashion. For example, the test report may indicate only whether or notthe TLE3 marker was detected, perhaps also with an indication of thelimits of detection. Additionally the test report may indicate thesubcellular location of binding, e.g., nuclear versus cytoplasmic and/orthe relative levels of binding in these different subcellular locations.The results may be presented in a semi-quantitative fashion. Forexample, various ranges may be defined and the ranges may be assigned ascore (e.g., 0 to 5) that provides a certain degree of quantitativeinformation. Such a score may reflect various factors, e.g., the numberof cells in which the marker is detected, the intensity of the signal(which may indicate the level of expression of the marker), etc. Theresults may be presented in a quantitative fashion, e.g., as apercentage of cells in which the marker is detected, as a concentration,etc. As will be appreciated by one of ordinary skill in the art, thetype of output provided by a test will vary depending upon the technicallimitations of the test and the biological significance associated withdetection of the marker. For example, in certain circumstances a purelyqualitative output (e.g., whether or not the marker is detected at acertain detection level) provides significant information. In othercases a more quantitative output (e.g., a ratio of the level ofexpression of the marker in two samples) is necessary.

Detecting TLE3 Polynucleotide Markers

Although in many cases detection of polypeptide markers usinginteraction partners such as antibodies may represent the mostconvenient means of determining whether TLE3 is expressed in aparticular sample, the inventive methods also encompass the use ofprimers for the detection of polynucleotide markers. A variety ofmethods for detecting the presence of a particular polynucleotide markerare known in the art and may be used in the inventive methods. Ingeneral, these methods rely on hybridization between one or more primersand the polynucleotide marker.

Any available strategy or system may be utilized to detect hybridizationbetween primers and the TLE3 polynucleotides (which could be a TLE3mRNA, a cDNA produced by RT-PCR from mRNA, RNA produced from such cDNA,etc.). In certain embodiments, hybridization can be detected by simplyadding a detectable label to the primer. In other embodiments,hybridization can be detected by using a labeled secondary primer thathybridizes specifically with the primary primer (e.g., a region of theprimary primer that does not hybridize with the TLE3 marker). In yetother embodiments it may be advantageous to amplify the TLE3 markerwithin the cancer sample by PCR using a set of primers designed toamplify a region of the TLE3 gene. The resulting product can then bedetected, e.g., using a labeled secondary primer that hybridizes withthe amplified product. Those skilled in the art will appreciatevariations on these embodiments.

Considerations for primer design are well known in the art and aredescribed, for example, in Newton, et al. (eds.) PCR: Essential dataSeries, John Wiley & Sons; PCR Primer: A Laboratory Manual, Cold SpringHarbor Laboratory Press, Cold Spring Harbor, N.Y., 1995; White, et al.(eds.) PCR Protocols: Current methods and Applications, Methods inMolecular Biology, The Humana Press, Totowa, N.J., 1993. In addition, avariety of computer programs known in the art may be used to selectappropriate primers.

In general, a detectable label may be directly detectable or indirectlydetectable, e.g., through combined action with one or more additionalmembers of a signal producing system. Examples of directly detectablelabels include radioactive, paramagnetic, fluorescent, light scattering,absorptive and colorimetric labels. Examples of indirectly detectableinclude chemiluminescent labels, e.g., enzymes that are capable ofconverting a substrate to a chromogenic product such as alkalinephosphatase, horseradish peroxidase and the like.

Once a labeled primer has hybridized with the TLE3 marker, the complexmay be visualized or detected in a variety of ways, with the particularmanner of detection being chosen based on the particular detectablelabel, where representative detection means include, e.g., scintillationcounting, autoradiography, measurement of paramagnetism, fluorescencemeasurement, light absorption measurement, measurement of lightscattering and the like.

In general, hybridization between a primer and the TLE3 marker may beassayed by contacting the primer with a cancer sample that includes themarker. Depending upon the nature of the cancer sample, appropriatemethods include, but are not limited to, microarray analysis, in situhybridization, Northern blot, and various nucleic acid amplificationtechniques such as PCR, RT-PCR, quantitative PCR, the ligase chainreaction, etc.

Identification of Novel Therapies

The predictive power of TLE3 is useful according to the presentinvention not only to classify cancers with respect to their likelyresponsiveness to known therapies, but also to identify potential newtherapies or therapeutic agents that could be useful in the treatment ofcancer.

Indeed, TLE3 represents an attractive candidate for identification ofnew therapeutic agents (e.g., via screens to detect compounds orentities that bind or hybridize to the marker, preferably with at leasta specified affinity and/or specificity, and/or via screens to detectcompounds or entities that modulate (i.e., increase or decrease)expression, localization, modification, or activity of the marker. Thus,in one embodiment the present invention provides methods comprisingsteps of contacting a test compound with a cell expressing the TLE3marker (e.g., individual engineered cells or in the context of a tissue,etc.); and determining whether the test compound modulates theexpression, localization, modification, or activity of the TLE3 marker.In many instances, interaction partners or primers (e.g., antisense orRNAi primers) themselves may prove to be useful therapeutics.

Thus the present invention provides interaction partners and primersthat are themselves useful therapeutic agents. For example, binding byan antibody raised against TLE3 to cancerous cells might inhibit growthof those cells. Alternatively or additionally, interaction partnersdefined or prepared according to the present invention could be used todeliver a therapeutic agent to a cancer cell. In particular, interactionpartners (e.g., an antibody raised against TLE3) may be coupled to oneor more therapeutic agents. Suitable agents in this regard includeradionuclides and drugs. Preferred radionuclides include ⁹⁰Y, ¹²³I,¹²⁵I, ¹³¹I, ¹⁸⁶Re, ¹⁸⁸Re, ²¹¹At and ²¹²Bi. Preferred drugs includechlorambucil, ifosphamide, meclorethamine, cyclophosphamide,carboplatin, cisplatin, procarbazine, decarbazine, carmustine,cytarabine, hydroxyurea, mercaptopurine, methotrexate, paclitaxel,docetaxel, thioguanine, 5-fluorouracil, actinomycin D, bleomycin,daunorubicin, doxorubicin, etoposide, vinblastine, vincristine,L-asparginase, adrenocorticosteroids, canciclovir triphosphate, adeninearabinonucleoside triphosphate,5-aziridinyl-4-hydroxylamino-2-nitrobenzamide, acrolein, phosphoramidemustard, 6-methylpurine, etoposide, benzoic acid mustard, cyanide andnitrogen mustard.

According to such embodiments, the therapeutic agent may be coupled withan interaction partner by direct or indirect covalent or non-covalentinteractions. A direct interaction between a therapeutic agent and aninteraction partner is possible when each possesses a substituentcapable of reacting with the other. For example, a nucleophilic group,such as an amino or sulfhydryl group, on one may be capable of reactingwith a carbonyl-containing group, such as an anhydride or an acidhalide, or with an alkyl group containing a good leaving group (e.g., ahalide) on the other. Indirect interactions might involve a linker groupthat is itself non-covalently bound to both the therapeutic agent andthe interaction partner. A linker group can function as a spacer todistance an interaction partner from an agent in order to avoidinterference with association capabilities. A linker group can alsoserve to increase the chemical reactivity of a substituent on an agentor an interaction partner and thus increase the coupling efficiency. Anincrease in chemical reactivity may also facilitate the use of agents,or functional groups on agents, which otherwise would not be possible.

It will be evident to those skilled in the art that a variety ofbifunctional or polyfunctional reagents, both homo- andhetero-functional (such as those described in the catalog of the PierceChemical Co., Rockford, Ill.), may be employed as the linker group.Coupling may be effected, for example, through amino groups, carboxylgroups, sulfydryl groups or oxidized carbohydrate residues. There arenumerous references describing such methodology, e.g., U.S. Pat. No.4,671,958, to Rodwell et al. It will further be appreciated that atherapeutic agent and an interaction partner may be coupled vianon-covalent interactions, e.g., ligand/receptor type interactions. Anyligand/receptor pair with a sufficient stability and specificity tooperate in the context of the invention may be employed to couple atherapeutic agent and an interaction partner. To give but an example, atherapeutic agent may be covalently linked with biotin and aninteraction partner with avidin. The strong non-covalent binding ofbiotin to avidin would then allow for coupling of the therapeutic agentand the interaction partner. Typical ligand/receptor pairs includeprotein/co-factor and enzyme/substrate pairs. Besides the commonly usedbiotin/avidin pair, these include without limitation,biotin/streptavidin, digoxigenin/anti-digoxigenin, FK506/FK506-bindingprotein (FKBP), rapamycin/FKBP, cyclophilin/cyclosporin andglutathione/glutathione transferase pairs. Other suitableligand/receptor pairs would be recognized by those skilled in the art,e.g., monoclonal antibodies paired with a epitope tag such as, withoutlimitation, glutathione-S-transferase (GST), c-myc, FLAG® and maltosebinding protein (MBP) and further those described in Kessler pp. 105-152of Advances in Mutagenesis” Ed. by Kessler, Springer-Verlag, 1990;“Affinity Chromatography: Methods and Protocols (Methods in MolecularBiology)” Ed. by Pascal Baillon, Humana Press, 2000; and “ImmobilizedAffinity Ligand Techniques” by Hermanson et al., Academic Press, 1992.

Where a therapeutic agent is more potent when free from the interactionpartner, it may be desirable to use a linker group which is cleavableduring or upon internalization into a cell. A number of differentcleavable linker groups have been described. The mechanisms for theintracellular release of an agent from these linker groups includecleavage by reduction of a disulfide bond (e.g., U.S. Pat. No. 4,489,710to Spitler), by irradiation of a photolabile bond (e.g., U.S. Pat. No.4,625,014 to Senter et al.), by hydrolysis of derivatized amino acidside chains (e.g., U.S. Pat. No. 4,638,045 to Kohn et al.), by serumcomplement-mediated hydrolysis (e.g., U.S. Pat. No. 4,671,958 to Rodwellet al.) and by acid-catalyzed hydrolysis (e.g., U.S. Pat. No. 4,569,789to Blattler et al.).

In certain embodiments, it may be desirable to couple more than onetherapeutic agent to an interaction partner. In one embodiment, multiplemolecules of an agent are coupled to one interaction partner molecule.In another embodiment, more than one type of therapeutic agent may becoupled to one interaction partner molecule. Regardless of theparticular embodiment, preparations with more than one agent may beprepared in a variety of ways. For example, more than one agent may becoupled directly to an interaction partner molecule, or linkers thatprovide multiple sites for attachment can be used.

Alternatively, a carrier can be used. A carrier may bear the agents in avariety of ways, including covalent bonding either directly or via alinker group. Suitable carriers include proteins such as albumins (e.g.,U.S. Pat. No. 4,507,234 to Kato et al.), peptides, and polysaccharidessuch as aminodextran (e.g., U.S. Pat. No. 4,699,784 to Shih et al.). Acarrier may also bear an agent by non-covalent bonding or byencapsulation, such as within a liposome vesicle (e.g., U.S. Pat. No.4,429,008 to Martin et al. and U.S. Pat. No. 4,873,088 to Mayhew etal.). Carriers specific for radionuclide agents include radiohalogenatedsmall molecules and chelating compounds. For example, U.S. Pat. No.4,735,792 to Srivastava discloses representative radiohalogenated smallmolecules and their synthesis. A radionuclide chelate may be formed fromchelating compounds that include those containing nitrogen and sulfuratoms as the donor atoms for binding the metal, or metal oxide,radionuclide. For example, U.S. Pat. No. 4,673,562 to Davison et al.discloses representative chelating compounds and their synthesis.

When interaction partners are themselves therapeutics, it will beunderstood that, in many cases, any interaction partner that binds thesame marker may be so used.

In one preferred embodiment of the invention, the therapeutic agents(whether interaction partners or otherwise) are antibodies, e.g., anantibody against the TLE3 marker. As is well known in the art, whenusing an antibody or fragment thereof for therapeutic purposes it mayprove advantageous to use a “humanized” or “veneered” version of anantibody of interest to reduce any potential immunogenic reaction. Ingeneral, “humanized” or “veneered” antibody molecules and fragmentsthereof minimize unwanted immunological responses toward antihumanantibody molecules which can limit the duration and effectiveness oftherapeutic applications of those moieties in human recipients.

A number of “humanized” antibody molecules comprising an antigen bindingportion derived from a non-human immunoglobulin have been described inthe art, including chimeric antibodies having rodent variable regionsand their associated complementarity-determining regions (CDRs) fused tohuman constant domains (e.g., see Winter et al., Nature 349:293, 1991;Lobuglio et al., Proc. Nat. Acad. Sci. USA 86:4220, 1989; Shaw et al.,J. Immunol. 138:4534, 1987; and Brown et al., Cancer Res. 47:3577,1987), rodent CDRs grafted into a human supporting framework region (FR)prior to fusion with an appropriate human antibody constant domain(e.g., see Riechmann et al., Nature 332:323, 1988; Verhoeyen et al.,Science 239:1534, 1988; and Jones et al. Nature 321:522, 1986) androdent CDRs supported by recombinantly veneered rodent FRs (e.g., seeEuropean Patent Publication No. 519,596, published Dec. 23, 1992). It isto be understood that the invention also encompasses “fully human”antibodies produced using the XenoMouse™ technology (AbGenix Corp.,Fremont, Calif.) according to the techniques described in U.S. Pat. No.6,075,181.

Yet further, so-called “veneered” antibodies may be used that include“veneered FRs”. The process of veneering involves selectively replacingFR residues from, e.g., a murine heavy or light chain variable region,with human FR residues in order to provide a xenogeneic moleculecomprising an antigen binding portion which retains substantially all ofthe native FR protein folding structure. Veneering techniques are basedon the understanding that the antigen binding characteristics of anantigen binding portion are determined primarily by the structure andrelative disposition of the heavy and light chain CDR sets within theantigen-association surface (e.g., see Davies et al., Ann. Rev. Biochem.59:439, 1990). Thus, antigen association specificity can be preserved ina humanized antibody only wherein the CDR structures, their interactionwith each other and their interaction with the rest of the variableregion domains are carefully maintained. By using veneering techniques,exterior (e.g., solvent-accessible) FR residues which are readilyencountered by the immune system are selectively replaced with humanresidues to provide a hybrid molecule that comprises either a weaklyimmunogenic, or substantially non-immunogenic veneered surface.

Preferably, interaction partners suitable for use as therapeutics (ortherapeutic agent carriers) exhibit high specificity for the targetmarker (e.g., TLE3) and low background binding to other markers. Incertain embodiments, monoclonal antibodies are preferred for therapeuticpurposes.

Pharmaceutical Compositions

As mentioned above, the present invention provides new therapies andmethods for identifying these. In certain embodiments, an interactionpartner or primer may be a useful therapeutic agent. Alternatively oradditionally, interaction partners defined or prepared according to thepresent invention bind to markers (e.g., TLE3) that serve as targets fortherapeutic agents. Also, inventive interaction partners may be used todeliver a therapeutic agent to a cancer cell. For example, interactionpartners provided in accordance with the present invention may becoupled to one or more therapeutic agents.

The invention includes pharmaceutical compositions comprising theseinventive therapeutic agents. In general, a pharmaceutical compositionwill include a therapeutic agent in addition to one or more inactiveagents such as a sterile, biocompatible carrier including, but notlimited to, sterile water, saline, buffered saline, or dextrosesolution. The pharmaceutical compositions may be administered eitheralone or in combination with other therapeutic agents including otherchemotherapeutic agents, hormones, vaccines and/or radiation therapy. By“in combination with”, here and elsewhere in the specification, it isnot intended to imply that the agents must be administered at the sametime or formulated for delivery together, although these methods ofdelivery are within the scope of the invention. In general, each agentwill be administered at a dose and on a time schedule determined forthat agent. Additionally, the invention encompasses the delivery of theinventive pharmaceutical compositions in combination with agents thatmay improve their bioavailability, reduce or modify their metabolism,inhibit their excretion, or modify their distribution within the body.Although the pharmaceutical compositions of the present invention can beused for treatment of any subject (e.g., any animal) in need thereof,they are most preferably used in the treatment of humans.

The pharmaceutical compositions of this invention can be administered tohumans and other animals by a variety of routes including oral,intravenous, intramuscular, intra-arterial, subcutaneous,intraventricular, transdermal, rectal, intravaginal, intraperitoneal,topical (as by powders, ointments, or drops), bucal, or as an oral ornasal spray or aerosol. In general the most appropriate route ofadministration will depend upon a variety of factors including thenature of the agent (e.g., its stability in the environment of thegastrointestinal tract), the condition of the patient (e.g., whether thepatient is able to tolerate oral administration), etc. At present theintravenous route is most commonly used to deliver therapeuticantibodies. However, the invention encompasses the delivery of theinventive pharmaceutical composition by any appropriate route takinginto consideration likely advances in the sciences of drug delivery.

General considerations in the formulation and manufacture ofpharmaceutical agents may be found, for example, in Remington'sPharmaceutical Sciences, 19^(th) ed., Mack Publishing Co., Easton, Pa.,1995.

EXEMPLIFICATION Example 1 Raising Antibodies

This example describes a method that was employed to generate the TLE3antibodies used in these Examples. Similar methods may be used togenerate an antibody that binds to any marker of interest (e.g., toproteins that are or are derived from other markers listed in AppendixA). In some cases, antibodies may be obtained from commercial sources(e.g., Chemicon, Dako, Oncogene Research Products, NeoMarkers, etc.) orother publicly available sources (e.g., Imperial Cancer ResearchTechnology, etc.).

Materials and Solutions

-   -   Anisole (Cat. No. A4405, Sigma, St. Louis, Mo.)    -   2,2′-azino-di-(3-ethyl-benzthiazoline-sulfonic acid) (ABTS)        (Cat. No. A6499, Molecular Probes, Eugene, Oreg.)    -   Activated maleimide Keyhole Limpet Hemocyanin (Cat. No. 77106,        Pierce, Rockford, Ill.)    -   Keyhole Limpet Hemocyanin (Cat. No. 77600, Pierce, Rockford,        Ill.)    -   Phosphoric Acid (H₃PO₄) (Cat. No. P6560, Sigma)    -   Glacial Acetic Acid (Cat No. BP1185-500, Fisher)    -   EDC (EDAC) (Cat No. 341006, Calbiochem)    -   25% Glutaraldehyde (Cat No. G-5882, Sigma)    -   Glycine (Cat No. G-8898, Sigma)    -   Biotin (Cat. No. B2643, Sigma)    -   Boric acid (Cat. No. B0252, Sigma)    -   Sepharose 4B (Cat. No. 17-0120-01, LKB/Pharmacia, Uppsala,        Sweden)    -   Bovine Serum Albumin (LP) (Cat. No. 100 350, Boehringer        Mannheim, Indianapolis, Ind.)    -   Cyanogen bromide (Cat. No. C6388, Sigma)    -   Dialysis tubing Spectra/Por Membrane MWCO: 6-8,000 (Cat. No. 132        665, Spectrum Industries, Laguna Hills, Calif.)    -   Dimethyl formamide (DMF) (Cat. No. 22705-6, Aldrich, Milwaukee,        Wis.)    -   DIC (Cat. No. BP 592-500, Fisher)    -   Ethanedithiol (Cat. No. 39, 802-0, Aldrich)    -   Ether (Cat. No. TX 1275-3, EM Sciences)    -   Ethylenediaminetetraacetatic acid (EDTA) (Cat. No. BP 120-1,        Fisher, Springfield, N.J.)    -   1-ethyl-3-(3′ dimethylaminopropyl)-carbodiimide, HCL (EDC) (Cat.        no. 341-006, Calbiochem, San Diego, Calif.)    -   Freund's Adjuvant, complete (Cat. No. M-0638-50B, Lee        Laboratories, Grayson, Ga.)    -   Freund's Adjuvant, incomplete (Cat. No. M-0639-50B, Lee        Laboratories)    -   Fritted chromatography columns (Column part No. 12131011; Frit        Part No. 12131029, Varian Sample Preparation Products, Harbor        City, Calif.)    -   Gelatin from Bovine Skin (Cat. No. G9382, Sigma)    -   Goat anti-rabbit IgG, biotinylated (Cat. No. A 0418, Sigma)    -   HOBt (Cat. No. 01-62-0008, Calbiochem)    -   Horseradish peroxidase (HRP) (Cat. No. 814 393, Boehringer        Mannheim)    -   HRP-Streptavidin (Cat. No. S 5512, Sigma)    -   Hydrochloric Acid (Cat. No. 71445-500, Fisher)    -   Hydrogen Peroxide 30% w/w (Cat. No. H1009, Sigma)    -   Methanol (Cat. No. A412-20, Fisher)    -   Microtiter plates, 96 well (Cat. No. 2595, Corning-Costar,        Pleasanton, Calif.)    -   N— -Fmoc protected amino acids from Calbiochem. See '97-'98        Catalog pp. 1-45.    -   N— -Fmoc protected amino acids attached to Wang Resin from        Calbiochem. See '97-'98 Catalog pp. 161-164.    -   NMP (Cat. No. CAS 872-50-4, Burdick and Jackson, Muskegon,        Mich.)    -   Peptide (Synthesized by Research Genetics. Details given below)    -   Piperidine (Cat. No. 80640, Fluka, available through Sigma)    -   Sodium Bicarbonate (Cat. No. BP328-1, Fisher)    -   Sodium Borate (Cat. No. B9876, Sigma)    -   Sodium Carbonate (Cat. No. BP357-1, Fisher)    -   Sodium Chloride (Cat. No. BP 358-10, Fisher)    -   Sodium Hydroxide (Cat. No. SS 255-1, Fisher)    -   Streptavidin (Cat. No. 1 520, Boehringer Mannheim)    -   Thioanisole (Cat. No. T-2765, Sigma)    -   Trifluoroacetic acid (Cat. No. TX 1275-3, EM Sciences)    -   Tween-20 (Cat. No. BP 337-500, Fisher)    -   Wetbox (Rectangular Servin′ Saver™ Part No. 3862, Rubbermaid,        Wooster, Ohio)    -   BBS—Borate Buffered Saline with EDTA dissolved in distilled        water (pH 8.2 to 8.4 with HCl or NaOH), 25 mM Sodium borate        (Borax), 100 mM Boric Acid, 75 mM NaCl and 5 mM EDTA.    -   0.1 N HCl in saline as follows: concentrated HCl (8.3 ml/0.917        liter distilled water) and 0.154 M NaCl    -   Glycine (pH 2.0 and pH 3.0) dissolved in distilled water and        adjusted to the desired pH, 0.1 M glycine and 0.154 M NaCl.    -   5× Borate 1× Sodium Chloride dissolved in distilled water, 0.11        M NaCl, 60 mM Sodium Borate and 250 mM Boric Acid.    -   Substrate Buffer in distilled water adjusted to pH 4.0 with        sodium hydroxide, 50 to 100 mM Citric Acid.    -   AA solution: HOBt is dissolved in NMP (8.8 grams HOBt to 1 liter        NMP). Fmoc-N-α-amino at a concentration at 0.53 M.    -   DIC solution: 1 part DIC to 3 parts NMP.    -   Deprotecting solution: 1 part Piperidine to 3 parts DMF.    -   Reagent R: 2 parts anisole, 3 parts ethanedithiol, 5 parts        thioanisole and 90 parts trifluoroacetic acid.        Equipment    -   MRX Plate Reader (Dynatech, Chantilly, Va.)    -   Hamilton Eclipse (Hamilton Instruments, Reno, Nev.)    -   Beckman TJ-6 Centrifuge (Model No. TJ-6, Beckman Instruments,        Fullerton, Calif.)    -   Chart Recorder (Recorder 1 Part No. 18-1001-40, Pharmacia LKB        Biotechnology)    -   UV Monitor (Uvicord SII Part No. 18-1004-50, Pharmacia LKB        Biotechnology)    -   Amicon Stirred Cell Concentrator (Model 8400, Amicon, Beverly,        Mass.)    -   30 kD MW cut-off filter (Cat. No. YM-30 Membranes Cat. No.        13742, Amicon)    -   Multi-channel Automated Pipettor (Cat. No. 4880, Corning Costar,        Cambridge, Mass.)    -   pH Meter Corning 240 (Corning Science Products, Corning        Glassworks, Corning, N.Y.)    -   ACT396 peptide synthesizer (Advanced ChemTech, Louisville, Ky.)    -   Vacuum dryer (Box from Labconco, Kansas City, Mo. and Pump from        Alcatel, Laurel, Md.).    -   Lyophilizer (Unitop 600 sl in tandem with Freezemobile 12, both        from Virtis, Gardiner, N.Y.)        Peptide Selection

Peptide or peptides against which antibodies would be raised wereselected from within the protein sequence of interest using a programthat uses the Hopp/Woods method (described in Hopp and Woods, Mol.Immunol. 20:483, 1983 and Hopp and Woods, Proc. Nat. Acad. Sci. U.S.A.78:3824, 1981). The program uses a scanning window that identifiespeptide sequences of 15-20 amino acids containing several putativeantigenic epitopes as predicted by low solvent accessibility. This is incontrast to most implementations of the Hopp/Woods method, whichidentify single short (˜6 amino acids) presumptive antigenic epitopes.Occasionally the predicted solvent accessibility was further assessed byPHD prediction of loop structures (described in Rost and Sander,Proteins 20:216, 1994). Preferred peptide sequences display minimalsimilarity with additional known human proteins. Similarity wasdetermined by performing BLASTP alignments, using a wordsize of 2(described in Altschul et al., J. Mol. Biol. 215:403, 1990). Allalignments given an EXPECT value less than 1000 were examined andalignments with similarities of greater than 60% or more than fourresidues in an exact contiguous non-gapped alignment forced thosepeptides to be rejected. When it was desired to target regions ofproteins exposed outside the cell membrane, extracellular regions of theprotein of interest were determined from the literature or as defined bypredicted transmembrane domains using a hidden Markov model (describedin Krogh et al., J. Mol. Biol. 305:567, 2001). When the peptide sequencewas in an extracellular domain, peptides were rejected if they containedN-linked glycosylation sites. As shown in Appendix A, for thepreparation of TLE3 antibodies a single peptide was used having theamino acid sequence KNHHELDHRERESSAN (SEQ ID NO. 383). Appendix Aprovides one to three peptide sequences that can be used in preparingantibodies against other markers.

Peptide Synthesis

The sequence of the desired peptide was provided to the peptidesynthesizer. The C-terminal residue was determined and the appropriateWang Resin was attached to the reaction vessel. The peptide or peptideswere synthesized C-terminus to N-terminus by adding one amino acid at atime using a synthesis cycle. Which amino acid is added was controlledby the peptide synthesizer, which looks to the sequence of the peptidethat was entered into its database. The synthesis steps were performedas follows:

Step 1—Resin Swelling: Added 2 ml DMF, incubated 30 minutes, drainedDMF.

Step 2—Synthesis cycle (repeated over the length of the peptide)

-   -   2a—Deprotection: 1 ml deprotecting solution was added to the        reaction vessel and incubated for 20 minutes.    -   2b—Wash Cycle    -   2c—Coupling: 750 ml of amino acid solution (changed as the        sequence listed in the peptide synthesizer dictated) and 250 ml        of DIC solution were added to the reaction vessel. The reaction        vessel was incubated for thirty minutes and washed once. The        coupling step was repeated once.    -   2d—Wash Cycle

Step 3—Final Deprotection: Steps 2a and 2b were performed one last time.

Resins were deswelled in methanol (rinsed twice in 5 ml methanol,incubated 5 minutes in 5 ml methanol, rinsed in 5 ml methanol) and thenvacuum dried.

Peptide was removed from the resin by incubating 2 hours in reagent Rand then precipitated into ether. Peptide was washed in ether and thenvacuum dried. Peptide was resolubilized in diH₂O, frozen and lyophilizedovernight.

Conjugation of Peptide with Keyhole Limpet Hemocyanin

Peptide (6 mg) was conjugated with Keyhole Limpet Hemocyanin (KLH). Ifthe selected peptide includes at least one cysteine, three aliquots (2mg) can be dissolved in PBS (2 ml) and coupled to KLH viaglutaraldehyde, EDC or maleimide activated KLH (2 mg) in 2 ml of PBS fora total volume of 4 ml. When the peptide lacks cysteine (as in the TLE3peptide), two aliquots (3 mg) can be coupled via glutaraldehyde and EDCmethods.

Maleimide coupling can be accomplished by mixing 2 mg of peptide with 2mg of maleimide-activated KLH dissolved in PBS (4 ml) and incubating 4hr.

EDC coupling can be accomplished by mixing 2 mg of peptide, 2 mgunmodified KLH, and 20 mg of EDC in 4 ml PBS (lowered to pH 5 by theaddition of phosphoric acid), and incubating for 4 hours. The reactionis then stopped by the slow addition of 1.33 ml acetic acid (pH 4.2).When using EDC to couple 3 mg of peptide, the amounts listed above areincreased by a factor of 1.5.

Glutaraldehyde coupling occurs when 2 mg of peptide are mixed with 2 mgof KLH in 0.9 ml of PBS. 0.9 ml of 0.2% glutaraldehyde in PBS is addedand mixed for one hour. 0.46 ml of 1 M glycine in PBS is added and mixedfor one hour. When using glutaraldehyde to couple 3 mg of peptide, theabove amounts are increased by a factor of 1.5.

The conjugated aliquots were subsequently repooled, mixed for two hours,dialyzed in 1 liter PBS and lyophilized.

Immunization of Rabbits

Two New Zealand White Rabbits were injected with 250 μg (total) KLHconjugated peptide in an equal volume of complete Freund's adjuvant andsaline in a total volume of 1 ml. 100 μg KLH conjugated peptide in anequal volume of incomplete Freund's Adjuvant and saline were theninjected into three to four subcutaneous dorsal sites for a total volumeof 1 ml two, six, eight and twelve weeks after the first immunization.The immunization schedule was as follows:

Day 0 Pre-immune bleed, primary immunization Day 15 1st boost Day 27 1stbleed Day 44 2nd boost Day 57 2nd bleed and 3rd boost Day 69 3rd bleedDay 84 4th boost Day 98 4th bleedCollection of Rabbit Serum

The rabbits were bled (30 to 50 ml) from the auricular artery. The bloodwas allowed to clot at room temperature for 15 minutes and the serum wasseparated from the clot using an IEC DPR-6000 centrifuge at 5000 g.Cell-free serum was decanted gently into a clean test tube and stored at−20° C. for affinity purification.

Determination of Antibody Titer

All solutions with the exception of wash solution were added by theHamilton Eclipse, a liquid handling dispenser. The antibody titer wasdetermined in the rabbits using an ELISA assay with peptide on the solidphase. Flexible high binding ELISA plates were passively coated withpeptide diluted in BBS (100 μl, 1 μg/well) and the plate was incubatedat 4° C. in a wetbox overnight (air-tight container with moistenedcotton balls). The plates were emptied and then washed three times withBBS containing 0.1% Tween-20 (BBS-TW) by repeated filling and emptyingusing a semi-automated plate washer. The plates were blocked bycompletely filling each well with BBS-TW containing 1% BSA and 0.1%gelatin (BBS-TW-BG) and incubating for 2 hours at room temperature. Theplates were emptied and sera of both pre- and post-immune serum wereadded to wells. The first well contained sera at 1:50 in BBS. The serawere then serially titrated eleven more times across the plate at aratio of 1:1 for a final (twelfth) dilution of 1:204,800. The plateswere incubated overnight at 4° C. The plates were emptied and washedthree times as described.

Biotinylated goat anti-rabbit IgG (100 μl) was added to each microtiterplate test well and incubated for four hours at room temperature. Theplates were emptied and washed three times. Horseradishperoxidase-conjugated Streptavidin (100 μl diluted 1:10,000 inBBS-TW-BG) was added to each well and incubated for two hours at roomtemperature. The plates were emptied and washed three times. The ABTSwas prepared fresh from stock by combining 10 ml of citrate buffer (0.1M at pH 4.0), 0.2 ml of the stock solution (15 mg/ml in water) and 10 μlof 30% hydrogen peroxide. The ABTS solution (100 μl) was added to eachwell and incubated at room temperature. The plates were read at 414 nm,20 minutes following the addition of substrate.

Preparation of Peptide Affinity Purification Column:

The affinity column was prepared by conjugating 5 mg of peptide to 10 mlof cyanogen bromide-activated Sepharose 4B and 5 mg of peptide tohydrazine-Sepharose 4B. Briefly, 100 μl of DMF was added to peptide (5mg) and the mixture was vortexed until the contents were completelywetted. Water was then added (900 μl) and the contents were vortexeduntil the peptide dissolved. Half of the dissolved peptide (500 μl) wasadded to separate tubes containing 10 ml of cyanogen-bromide activatedSepharose 4B in 0.1 ml of borate buffered saline at pH 8.4 (BBS) and 10ml of hydrazine-Sepharose 4B in 0.1 M carbonate buffer adjusted to pH4.5 using excess EDC in citrate buffer pH 6.0. The conjugation reactionswere allowed to proceed overnight at room temperature. The conjugatedSepharose was pooled and loaded onto fitted columns, washed with 10 mlof BBS, blocked with 10 ml of 1 M glycine and washed with 10 ml 0.1 Mglycine adjusted to pH 2.5 with HCl and re-neutralized in BBS. Thecolumn was washed with enough volume for the optical density at 280 nmto reach baseline.

Affinity Purification of Antibodies

The peptide affinity column was attached to a UV monitor and chartrecorder. The titered rabbit antiserum was thawed and pooled. The serumwas diluted with one volume of BBS and allowed to flow through thecolumns at 10 ml per minute. The non-peptide immunoglobulins and otherproteins were washed from the column with excess BBS until the opticaldensity at 280 nm reached baseline. The columns were disconnected andthe affinity purified column was eluted using a stepwise pH gradientfrom pH 7.0 to 1.0. The elution was monitored at 280 nm and fractionscontaining antibody (pH 3.0 to 1.0) were collected directly into excess0.5 M BBS. Excess buffer (0.5 M BBS) in the collection tubes served toneutralize the antibodies collected in the acidic fractions of the pHgradient.

The entire procedure was repeated with “depleted” serum to ensuremaximal recovery of antibodies. The eluted material was concentratedusing a stirred cell apparatus and a membrane with a molecular weightcutoff of 30 kD. The concentration of the final preparation wasdetermined using an optical density reading at 280 nm. The concentrationwas determined using the following formula: mg/ml=OD₂₈₀/1.4.

It will be appreciated that in certain embodiments, additional steps maybe used to purify antibodies of the invention. In particular, it mayprove advantageous to repurify antibodies, e.g., against one of thepeptides that was used in generating the antibodies. It is to beunderstood that the present invention encompasses antibodies that havebeen prepared with such additional purification or repurification steps.It will also be appreciated that the purification process may affect thebinding between samples and the inventive antibodies.

Example 2 Preparing and Staining Tissue Arrays

This example describes a method that was employed to prepare the tissuearrays that were used in the Examples. This example also describes howthe antibody staining was performed.

Tissue arrays were prepared by inserting full-thickness cores from alarge number of paraffin blocks (donor blocks) that contain fragments oftissue derived from many different patients and/or different tissues orfragments of tissues from a single patient, into a virgin paraffin block(recipient block) in a grid pattern at designated locations in a grid. Astandard slide of the paraffin embedded tissue (donor block) was thenmade which contained a thin section of the specimen amenable to H & Estaining A trained pathologist, or the equivalent versed in evaluatingtumor and normal tissue, designated the region of interest for samplingon the tissue array (e.g., a tumor area as opposed to stroma). Acommercially available tissue arrayer from Beecher Instruments was thenused to remove a core from the donor block which was then inserted intothe recipient block at a designated location. The process was repeateduntil all donor blocks had been inserted into the recipient block. Therecipient block was then thin-sectioned to yield 50-300 slidescontaining cores from all cases inserted into the block.

The selected antibodies were then used to perform immunohistochemicalstaining using the DAKO Envision+, Peroxidase IHC kit (DAKO Corp.,Carpenteria, Calif.) with DAB substrate according to the manufacturer'sinstructions. FIG. 1 shows exemplary IHC staining images of samples thatare TLE3-negative (S0643−) and TLE3-positive (S0643+).

Example 3 TLE3 Expression Correlates with Response to Chemotherapy inCancer Patients

Tumor samples from two different breast cancer cohorts—HuntsvilleHospital (HH) and Roswell Park Cancer Institute (RP)—were stained withthe TLE3 antibody of Example 1. Treatment and recurrence data wereavailable for all patients in both cohorts. FIG. 2 shows Kaplan-Meierrecurrence curves that were generated using all patients in the HHcohort after classification based on staining with the TLE3 antibody.Recurrence data from TLE3-positive and TLE3-negative patients were usedto generate the top and bottom curves, respectively. As shown in theFigure, antibody binding to the TLE3 marker correlates with improvedprognosis across this breast cancer cohort (HR=0.573, p=0.004). FIG. 3shows Kaplan-Meier recurrence curves that were generated in a similarfashion using all patients in the RP cohort. As with the HH cohort,antibody binding to the TLE3 marker was found to correlate with improvedprognosis (HR=0.239, p=0.011).

In order to determine whether TLE3 expression is correlated withresponse to chemotherapy, separate Kaplan-Meier recurrence curves weregenerated using HH cohort patients that did or did not receivechemotherapy (FIGS. 4 and 5, respectively). As shown in FIG. 4, antibodybinding to the TLE3 marker lost its correlation with prognosis inpatients that did not receive chemotherapy (HR=0.788, p=0.490). However,as shown in FIG. 5, the correlation was restored in patients that didreceive chemotherapy (HR=0.539, p=0.013). These results demonstrate thatTLE3 expression is correlated with improved response to chemotherapy(i.e., TLE3-positive cancers are more likely to respond to chemotherapythan TLE-3 negative cancers). Kaplan-Meier recurrence curves that weregenerated using patients in the RP breast cancer cohort that receivedchemotherapy are consistent with this prediction model (see FIG. 6,HR=0.194, p=0.010). Kaplan-Meier recurrence curves that were generatedusing patients in the UAB ovarian cancer cohort that receivedchemotherapy are also consistent with this prediction model (see FIG.18, HR=0.64, p=0.049).

Example 4 Specific Chemotherapeutic Correlations

Since different patients in the HH and RP cohorts received differenttypes of chemotherapy we were also able to determine whether TLE3expression correlates with response to specific types of chemotherapy.

FIG. 7 shows Kaplan-Meier recurrence curves that were generated usingpatients in the HH breast cancer cohort of FIG. 5 that received CMF(cyclophosphamide, methotrexate and 5-fluorouracil) chemotherapy.Recurrence data from TLE3-positive and TLE3-negative patients in thissubset were used to generate the top and bottom curves, respectively. Asshown in FIG. 7, antibody binding to the TLE3 marker correlates withimproved prognosis across this subset of treated patients (HR=0.398,p=0.019). Based on the results below which demonstrated a loss ofcorrelation for patients in the HH cohort that were treated with CA(cyclophosphamide and adriamycin, HR=1.000) or CAF (cyclophosphamide,adriamycin and 5-fluorouracil, HR=1.000) we were able to establish thatthe predictive correlation in FIG. 7 is between TLE3 binding andtreatment with methotrexate (see also FIG. 9 which combines the CA andCAF treated subsets, HR=1.030).

FIG. 8 shows Kaplan-Meier recurrence curves that were generated usingpatients in the HH breast cancer cohort of FIG. 5 that received CA orCAF chemotherapy (with or without a taxane). As shown in the Figure, thecorrelation between antibody binding to the TLE3 marker and prognosisloses significance in this subset of treated patients (HR=0.666,p=0.22). When the curves were generated using patients that received CAor CAF chemotherapy only (i.e., without a taxane) the significance wasfurther reduced (see FIG. 9, HR=1.030, p=0.95). However, the correlationwas restored in patients that received CA or CAF in combination with ataxane (see FIG. 10, HR=0.114, p=0.038). These results demonstrate acorrelation between TLE3 binding and treatment with a taxane.

FIG. 11 shows Kaplan-Meier recurrence curves that were generated usingpatients in the RP breast cancer cohort of FIG. 6 that received CAchemotherapy only (i.e., without a taxane). Recurrence data fromTLE3-positive and TLE3-negative patients in this subset were used togenerate the top and bottom curves, respectively. As shown in theFigure, there is no correlation between antibody binding to the TLE3marker and prognosis in this subset of treated patients (HR=0.759,p=0.81). The correlation was restored when the curves were generatedusing patients that received CA chemotherapy in combination with ataxane (see FIG. 12, HR=0.153, p=0.018). These results support theresults of FIGS. 8 and 9 that were obtained using samples from the HHcohort.

FIG. 13 shows Kaplan-Meier recurrence curves that were generated usingpatients in the RP breast cancer cohort of FIG. 6 that received a taxaneor CMF. Some of the patients receiving a taxane also received CA.Recurrence data from TLE3-positive and TLE3-negative patients in thissubset were used to generate the top and bottom curves, respectively. Asshown in the Figure, antibody binding to the TLE3 marker correlates withimproved prognosis across this subset of treated patients (HR=0.137,p=0.011).

FIG. 14 shows Kaplan-Meier recurrence curves that were generated usingpatients in the RP breast cancer cohort of FIG. 6 that receivedneoadjuvant chemotherapy. Recurrence data from TLE3-positive andTLE3-negative patients in this subset were used to generate the top andbottom curves, respectively. The sample size was small (N=12); however,as shown in the Figure, antibody binding to the TLE3 marker showedsignificant correlation with improved prognosis across this subset oftreated patients when measured using the Fisher Exact Test (p=0.005). Inaddition, of the 12 patients receiving neoadjuvant chemotherapy, tworeceived CA (both showed recurrence) while ten received CA with a taxane(seven showed recurrence, three did not). Notably, the three patientsthat did not show any recurrence were the only patients withTLE3-positive samples. These results are significant since they showthat the correlation between TLE3 binding and response to chemotherapyapplies irrespective of whether treatment is administered in an adjuvantor neoadjuvant setting.

FIGS. 15-17 show Kaplan-Meier recurrence curves that were generatedusing patients in the RP breast cancer cohort of FIG. 6 that receivedchemotherapy. Recurrence data from TLE3-positive and TLE3-negativepatients with stage II+ (FIG. 15), stage IIb+ (FIG. 16) and stage III+(FIG. 17) cancers were used to generate the top and bottom curves,respectively. In each case, antibody binding to the TLE3 markercorrelated with improved prognosis across these subsets of treatedpatients. The sample size was small in the subset of FIG. 17 (N=19);however significance was obtained when measured using the Fisher ExactTest (p=0.020). These results are of clinical importance since theydemonstrate that the predictive power of the TLE3 marker is independentof stage and remains significant even in patients with the worstprognosis (e.g., stage III+ patients).

Example 5 Bivariate Analysis

In order to confirm that the predictive power of TLE3 is independent ofother clinical factors (e.g., age, tumor size, nodes status, necrosis,etc.) we performed bivariate statistical analysis using results from theRP breast cohort. The results are summarized in Table 1 below. As shownin the Table, prediction using TLE3 remained significant in allbivariate analyses demonstrating its independence of other clinicalfactors.

TABLE 1 Bivariate Analysis HR for p for Factor 1 Factor 2 N TLE3 TLE3 HRP TLE3 — 81 0.239 0.0110 — — TLE3 Age 81 0.223 0.0082 0.967 0.1200 TLE3Tumor Size 78 0.219 0.0077 1.292 0.0002 TLE3 Nodes Met Ca¹ 79 0.2520.0150 1.066 0.0086 TLE3 Necrosis 72 0.232 0.0100 1.903 0.2600 TLE3Vase. Lymph Inv.² 74 0.205 0.0071 0.412 0.0790 TLE3 Stage 80 0.2840.0280 2.063 0.0130 TLE3 Contains Tax³ 70 0.168 0.0061 2.749 0.0980¹Nodes found with metastatic cancer. ²Vascular lymphatic invasion.³Taxane containing regimens.

APPENDIX A ENTREZ PEPTIDE  PEPTIDE  PEPTIDE  AGI GENE 1 (SEQ  2 (SEQ 3 (SEQ  ID GENE NAME ID ALIASES ID NO.) ID NO.) ID NO.) TITER S0011vav 3 oncogene 10451 VAV3; VAV3 ONCOGENE; TEESINDED EKRTNGL DYISKSK1:90- ONCOGENE VAV3; vav 3 oncogene IYKGLPDLI RRTPKQV EDVKLK  1:300DE (1) D (2) (3) S0017 WAP four- 10406 WFDC2; WAP5; dJ461P17.6; majorEKTGVCPE PNDKEGS RDQCQVD 1:25- disulfide core epididymis-specific protein E4; LQADQNCT CPQVNIN TQCPGQM 1:500 domain 2epididymal secretory protein E4; WAP  QE (4) (5) K (6)four-disulfide core domain 2; WAP domain containing protein HE4-V4;epididymis-specific, whey-acidic protein type, four-disulfide core; WAP four-disulfide S0018 secretoglobin,  4250 UGB2; MGB1; SCGB2A2;SKTINPQVS DDNATTN NQTDETL 1:300- family 2A,  mammaglobin 1; secretoglobin, family KTEYKELL AIDELKE SNVEVFM 1:1000member 2 2A, member 2 QE (7) C (8) Q (9) S0020 PPAR binding  5469RB18A; TRIP2; PPARGBP; PBP; SSDDGIRPL DGKSKDK NKTKKKK 1:100 proteinCRSP1; PPARBP; CRSP200; PEYSTEKH PPKRKKA SSRLPPE DRIP230; PPAR-BINDINGKK (10) DTE  K (12) PROTEIN; PPARG binding protein; (11)PPAR binding protein; CRSP, 200-KD SUBUNIT; PEROXISOMEPROLIFERATOR-ACTIVATED RECEPTOR-BINDING PROTEIN;THYROID HORMONE RECEPTOR INTERACTOR 2; RECOGN S0021 hypothetical  222256FLJ23834; hypothetical protein KNKEPLTK KLTCTDL EVDYENP 1:200- protein FLJ23834 KGETKTAE DSSPRSF SNLAAGN 1:2500 FLJ23834 RD (13) RYS (14)KYT (15) S0022 cytochrome   199974 CYP4Z1; cytochrome P450 4Z1; KTLQVFNPQHFAIIE RKFLAPD 1:50- P450 4Z1 cytochrome P450, family 4, sub- LRFSRENSE CKVAVAL HSRPPQP 1:500 family Z, polypeptide 1 KIH (16) T (17)VRQ  (18) S0024 RAS-like,  85004 RERG; RAS-like, estrogen-regulated,MAKSAEV VLPLKNI YELCREV 1:900- estrogen-  growth-inhibitor KLAIFGRALDEIKKP RRRRMVQ 1:2700 regulated, GVGK (19) KN (20) GKT (21) growth-inhibitor S0032 fatty acid  2170 MDGI; O-FABP; FABP3; FABP11; TKPTTIIEKKNTEISF HLQKWD 1:225 binding protein H-FABP; FATTY ACID-BINDING NGDILTLKKLGVEFD GQETTLV 3, muscle and  PROTEIN, SKELETAL MUSCLE; TH (22) E (23)RE (24) heart (mammary- Fatty acid-binding protein 3, muscle;derived growth fatty acid binding protein 11; FATTY inhibitor)ACID-BINDING PROTEIN, MUSCLE AND HEART; fatty acidbinding protein 3, muscle and heart (mammary-de S0036 gamma- 2568GABRP; GAMMA- DGNDVEFT LQQMAA KRKISFAS 1:250- aminobutyricAMINOBUTYRIC ACID WLRGNDS KDRGTTK IEISSDNV 1:500 acid (GABA) ARECEPTOR, PI; GABA-A VRGLEH EVEEVS DYSD  receptor, piRECEPTOR, PI POLYPEPTIDE; (25) (26) (27)gamma-aminobutyric acid (GABA) A receptor, pi S0037 annexin A8 244ANX8; ANXA8; annexin VIII; QRQQIAKS REIMKAY EEYEKIAN 1:30- annexin A8FKAQFGKD EEDYGSS KSIEDSIK 1:40 LTE (28) LEEDIQ SE (30) (29) S0039CDNA FLJ25076  134111 similar to 3110006E14Rik protein; EGGSLVPA RKAGKSKKTHEKYG 1:50- fis, clone  CDNA FLJ25076 fis, clone CBL06117 ARQQHCTQKSFSRKE WVTPPVS 1:30000 CBL06117 VRSRR (31) AE (32) DG (33) S0040ATP-binding  5243 P-gp; PGY1; CLCS; ABCB1; ABC20; MDLEGDR NLEDLMSRGSQAQD 1:200- cassette, sub- CD243; GP170; MDR1; doxorubicin NGGAKKKNITNRSD RKLSTKE 1:400 family B (MDR/ resistance; colchicin sensitivity;  N (34) INDTG  A (36) TAP), member 1P-GLYCOPROTEIN 1; multidrug (35) resistance 1; P glycoprotein 1; ATP-binding cassette sub-family B member 1; ATP-BINDING CASSETTE,SUBFAMILY B, MEMBER 1; ATP- bin S0041 ATP-binding  5244MDR3; PGY3; PFIC-3; ABCB4; MDLEAAK NFSFPVN KNSQMCQ 1:60- cassette, sub-ABC21; MDR2/3; P- NGTAWRPT FSLSLLN KSLDVET 1:300 family B (MDR/ GLYCOPROTEIN 3; MULTIDRUG SAE (37) PGK  DG (39) TAP), member 4RESISTANCE 3; P-glycoprotein- (38) 3/multiple drug resistance-3; Pglycoprotein 3/multiple drug  resistance 3; ATP-binding cassette, sub-family B (MDR/TAP), member 4;  ATP-binding cassette, sub S0042ATP-binding  4363 ABCC1; MRP1; GS-X; ABC29; MALRGFCS KNWKKE DSIERRPV1:40- cassette, sub- multidrug resistance protein; ADGSD  CAKTRKQKDGGGTN 1:500 family C (CFTR/ MULTIDRUG RESISTANCE- (40) PVK  S (42)MRP), member 1 ASSOCIATED PROTEIN 1; multiple (41)drug resistance-associated protein; multiple drug resistance protein 1;ATP-BINDING CASSETTE, SUBFAMILY C, MEMBER 1; ATP-binding cassette, sub-fami S0043 ATP-binding   1244MRP2; cMRP; CMOAT; ABCC2; MLEKFCNS SILCGTF ENNESSN 1:50- cassette, sub-ABC30; DJS; MULTIDRUG TFWNSSFL QFQTLIR NPSSIAS 1:333 family C (CFTR/RESISTANCE-ASSOCIATED DSPE (43) T (44) (45) MRP), member 2PROTEIN 2; canalicular multispecific organic anion transporter;MULTISPECIFIC ORGANIC ANION TRANSPORTER, CANALICULAR;ATP-BINDING CASSETTE, SUBFAMILY C, MEMBER 2; ATP- binding cassette,S0044 ATP-binding   10257 MOAT-B; MRP4; MOATB; ABCC4; QEVKPNPL DEISQRNVQDFTAF 1:20- cassette, sub- EST170205; MULTIDRUG QDANICSR RQLPSDGWDKASET 1:100 family C (CFTR/ RESISTANCE-ASSOCIATED (46) KK (47) PTLQ MRP), member 4 PROTEIN 4; MULTISPECIFIC (48) ORGANIC ANION TRANSPORTERB; ATP-binding cassette, sub-family C, member 4; ATP-BINDINGCASSETTE, SUBFAMILY C, MEMBER 4; ATP-binding cassette, sub-family C (CFTS0045 ATP-binding   8714 MOAT-D; ABC31; MLP2; ABCC3; MDALCGSG RKQEKQTDPQSVER 1:2000 cassette, sub- EST90757; cMOAT2; MULTIDRUG ELGSKFWDARHKASA KTISPG family C (CFTR/ RESISTANCE-ASSOCIATED SN (49) A (50) (51)MRP), member 3 PROTEIN 3; canicular multispecificorganic anion transporter; CANALICULAR MULTISPECIFICORGANIC ANION TRANSPORTER 2; ATP-BINDING CASSETTE,SUBFAMILY C, MEMBER 3; ATP- binding cas S0046  ATP-binding   10057MOAT-C; ABCC5; MRP5; MKDIDIGK RDREDSK SKHESSD 1:100- cassette, sub-EST277145; ABC33; SMRP; EYIIPSPGY FRRTRPL VNCRRLE 1:450 family C (CFTR/pABC11; MOATC; MULTIDRUG RS (52) ECQD  R (54) MRP), member 5RESISTANCE-ASSOCIATED (53) PROTEIN 5; canalicular multispecificorganic anion transporter C; ATP- binding cassette, sub-family C,member 5; ATP-BINDING CASSETTE, SUBFAMILY C, MEMBER 5; ATP-bi S0047ATP-binding   368 MRP6; ARA; EST349056; ABCC6; MAAPAEPC DPGVVDS HTLVAEN1:50 cassette, sub- MOATE; PXE; MLP1; ABC34; AGQGVWN SSSGSAA AMNAEKfamily C (CFTR/ ANTHRACYCLINE RESISTANCE- QTEPE  GKD  (57)MRP), member 6 ASSOCIATED PROTEIN; (55) (56) MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN 6; ATP- binding cassette, sub-family C,member 6; ATP-BINDING CASSETTE, SUBFAMILY C,MEMBER 6; ATP-binding cassette, S0048 ATP-binding   8647BSEP; ABCB11; PFIC-2; SPGP; MSDSVILRS TNSSLNQ QEVLSKI 1:600cassette, sub- PGY4; PFIC2; ABC16; SISTER OF P- IKKFGEEN NMTNGTR QHGHTIIfamily B (MDR/ GLYCOPROTEIN; bile salt export D (58) (59) S (60)TAP), member 11 pump; progressive familial intrahepatic cholestasis 2; ABC  member 16, MDR/TAP subfamily; ATP-BINDING CASSETTE,  SUBFAMILY B, MEMBER 11; ATP- binding cassette, sub-fam S0049 ATP-binding   23456MTABC2; EST20237; MABC2; M- GADDPSSV NAVASPE KPNGIYR 1:10-cassette, sub- ABC2; ABCB10; MITOCHONDRIAL TAEEIQR FPPRFNT KLMNKQS 1:25family B (MDR/ ABC PROTEIN 2; ATP-BINDING (61) (62) FISA TAP), member 10 CASSETTE, SUBFAMILY B, (63)MEMBER 10; ATP-binding cassette, sub-family B, member 10; ATP-binding cassette, sub-family B (MDR/TAP), member 10 S0050transporter 1,  6890 RING4; ABC17; D6S114E; ABCB2; MASSRCPA QGGSGNPEFVGDGI 1:80 ATP- binding   TAP1; APT1; PEPTIDE PRGCR  VRR  YNNTMGcassette, sub-  TRANSPORTER PSF1; (64) (65) HVHS  family B TRANSPORTER, ABC, MHC, 1; (66) (MDR/TAP) ABC transporter, MHC 1; antigenpeptide transporter 1; peptide  supply factor 1; ABC TRANSPORTER,MHC, 1; ATP-BINDING CASSETTE, SUBFAMILY B, MEMBER 2; TRANSPORTER S0052ATP-binding   6833 SUR1; MRP8; PHHI; ABC36; MPLAFCGS DHLGKEN EIREEQC1:25- cassette, sub- ABCC8; HRINS; sulfonylurea ENHSAAYR DVFQPKT APHEPTP1:150 family C (CFTR/ receptor (hyperinsulinemia); (67) QFLG  QG (69)MRP), member 8 SULFONYLUREA RECEPTOR, (68) BETA-CELL HIGH-AFFINITY;ATP-binding cassette, sub- family C, member 8; ATP-BINDINGCASSETTE, SUBFAMILY C, MEMBER 8; ATP-binding cassette, sub-family CS0053 ATP-binding  10060 ABCC9; ABC37; sulfonylurea MSLSFCGN QRVNETQDEIGDDS 1:25- cassette, sub- receptor 2A; ATP-BINDING NISS (70) NGTNNTTWRTGESS 1:50 family C (CFTR/ CASSETTE, SUBFAMILY C, GISE  LPFE MRP), member 9 MEMBER 9; ATP-binding cassette, (71) (72)sub-family C (CFTR/MRP), member 9; ATP-binding cassette, sub-family C, member 9 isoform SUR2B;  ATP-binding cassette, sub-familyC, member 9 isoform S0055 integral  9445 E25B; ABRI; E3-16; FBD; BRI2;MVKVTFNS QTIEENI HDKETYK 1:450- membrane  BRICD2B; ITM2B; BRI GENE;ALAQKEAK KIFEEEE LQRRETI 1:500 protein 2B BRICHOS domain containing 2B;KDEPK  VE (74) KGIQKRE integral membrane protein 2B (73) (75) S0057ankyrin 3,  288 ankyrin-G; ANK3; ankyrin-3, node of MAHAASQ HKKETESEGFKVKT 1:750 node of Ranvier  Ranvier; ankyrin 3 isoform 1;  LKKNRDLEDQDDEIE KKEIRHV (ankyrin G) ankyrin 3 isoform 2; ankyrin 3,  INAEE KTDRRQ EKKSHS node of Ranvier (ankyrin G) (76) (77) (78) S0058hypothetical  80004 FLJ21918; hypothetical protein ERALAAAQ TAGMKDLDPPRTVL 1:20 protein FLJ21918 RCHKKVM LSVFQAY QAPKEWV FLJ21918 KER (79)Q (80) CL (81) S0059 tripartite  23650 ATDC; TRIM29; tripartite motif-MEAADASR ELHLKPH EGEGLGQ 1:50- motif-containing 29; ataxia-telangiectasia SNGSSPEA LEGAAFR SLGNFKD 1:3000containing 29 group D-associated protein;   RDAR (82) DHQ  DLLN tripartite motif protein TRIM29  (83) (84)isoform alpha; tripartite motif  protein TRIM29 isoform beta S0059tripartite  23650 ATDC; TRIM29; tripartite motif- ELHLKPHL N/A N/A 1:30-P2 motif- containing 29; ataxia-telangiectasia EGAAFRDH 1:90containing 29 group D-associated protein;   Q (85)tripartite motif protein TRIM29  isoform alpha; tripartite motif protein TRIM29 isoform beta S0063 iroquois homeo- 79191IRX3; iroquois homeobox protein 3 GSEERGAG KIWSLAE KKLLKTA 1:200-box protein 3 RGSSGGRE TATSPDN FQPVPRR 1:1200 E (86) PRRS  PQNHLD (87)(88) S0068 RAS-like,  85004 RERG; RAS-like, estrogen-regulated, RRSSTTHVN/A N/A 1:500- estrogen-  growth-inhibitor KQAINKML 1:40000 regulated, TKISS  growth-inhibitor (89) S0070 G protein- 26996GPCR150; GPR160; putative G MRRKNTC NETILYF KVQIPAY 1:10-coupled receptor  protein-coupled receptor; G protein- QNFMEYFC PFSSHSSIEMNIPL 1:100 160 coupled receptor 160 ISLAF  YTVRSKK VILCQ  (90) (91)(92) S0072 S100 calcium  6279 CP-10; L1Ag; CALPROTECTIN; MLTELEKARDDLKKL KMGVAA 1:6500- binding protein  60B8AG; S100A8; MIF; CAGA; NIF;LNSIIDVYH LETECPQ HKKSHE 1:10000 A8 (calgranulin MRP8; MA387; CFAG; CGLA K (93) YIRKKGA ESHKE  A)S100A8/S100A9 COMPLEX; cystic D (94) (95)fibrosis antigen; S100 calcium- binding protein A8; S100 calcium binding protein A8 (calgranulin A) S0073 forkhead box A1 3169HNF3A; MGC33105; TCF3A; PESRKDPS HGLAPHE EQQHKLD 1:100-FOXA1; forkhead box A1; GASNPSAD SQLHLKG FKAYEQA 1:2700HEPATOCYTE NUCLEAR FACTOR S (96) D (97) LQYS 3-ALPHA; hepatocyte nuclear factor  (98) 3, alpha S0073 forkhead box A13169 HNF3A; MGC33105; TCF3A; HGLAPHES N/A N/A 1:50- P2FOXA1; forkhead box Al; QLHLKGD 1:450 HEPATOCYTE NUCLEAR FACTOR (99)3-ALPHA; hepatocyte nuclear factor  3, alpha S0074 trefoil factor  7033TFF3; trefoil factor 3 (intestinal); EEYVGLSA RVDCGYP VPWCFKP 1:2500-3 (intestinal) trefoil factor 3, HITF, human  NQCAVPAK HVTPKEC LQEAECT1:30000 intestinal trefoil factor DRVD (100) N (101) F (102) S0074trefoil factor  7033 TFF3; trefoil factor 3 (intestinal); VPWCFKPL N/AN/A 1:400- P3 3 (intestinal) trefoil factor 3, HITF, human  QEAECTF1:810 intestinal trefoil factor (103) S0076 keratin 17 3872PC2; PCHC1; KRT17; K17; KKEPVTTR QDGKVIS SSSIKGS 1:200 x1CYTOKERATIN 17; keratin 17 QVRTIVEE SREQVHQ SGLGGGS (104) TTR  S (106)(105) S0078 kynureninase  8942 3.7.1.3; XANTHURENICACIDURIA; DEEDKLRHKPREGEE EERGCQL 1:180- (L-kynurenine  KYNU; FRECFYIPK TLRIEDI TITFSVP1:200 hydrolase) HYDROXYKYNURENINURIA; IQD (107) LEVIEKE NKDVFQEKYNURENINASE DEFICIENCY; (108) (109) XANTHURENIC ACIDURIA;kynureninase (L-kynurenine hydrolase) S0079 solute carrier  25800SLC39A6; LIV-1 protein, estrogen DHNHAASG EEPAMEM QRYSREE 1:200-family 39 (zinc  regulated; solute carrier family 39 KNKRKALC KRGPLFSLKDAGVA 1:800 transporter), (zinc transporter), member 6; solute PDHD HLSSQNI TL  member 6 carrier family 39 (metal ion (110) (111) (112)transporter), member 6 S0081 N-acetyl-  9AAC1; 2.3.1.5; NAT 1; arylamine N- MDIEAYLE QMWQPLE FNISLQR 1:10-transferase 1  acetyltransferase-1; ACETYL- RIGYKKSR LISGKDQ KLVPKHG1:240 (arylamine N- CoA: ARYLAMINE N- NKLDLE PQVPCVF DRFFTI acetyl-ACETYLTRANSFERASE; (113) R (114) (115) transferase) ARYLAMINE N-ACETYLTRANSFERASE 1; N- acetyltransferase 1 (arylamine N-acetyltransferase); arylamide  acetylase 1 (N-acetyltransferase 1) S0086X-box binding  7494 XBP2; TREB5; XBP1; X-box-binding RQRLTHLS EKTHGLVQPPFLCQ 1:180- protein 1 protein-1; X BOX-BINDING PEEKALRR VENQELRWGRHQPS 1:400 PROTEIN 1; X BOX-BINDING KLKNR QRLGMD WKPLMNPROTEIN 2; X-box binding protein 1 (116) (117) (118) S0088 claudin 109071 CPETRL3; OSP-L; CLDN10; claudin NKITTEFFD FSISDNN EDFKTTN 1:333-10; claudin 10 isoform a; claudin 10 PLFVEQK KTPRYTY PSKQFDK 1:1000isoform b (119) NGAT  NAYV (120) (121) S0090 sparc/ 9806KIAA0275; testican-2; SPOCK2; EGDAKGLK EWCFCFW EEEGEAG 1:100-osteonectin, TESTICAN 2; EGETPGNF REKPPCL EADDGGY 1:800 cwcv and kazal- SPARC/OSTEONECTIN, CWCV, MEDE  AELER IW  like domainsAND KAZAL-LIKE DOMAINS (122) (123) (124) proteoglycan PROTEOGLYCAN 2;(testican) 2 sparc/osteonectin, cwcv and kazal-like domains proteoglycan  (testican) 2 S0091 lipocalin 2  3934UTEROCALIN; NGAL; LCN2; DKDPQKM KKCDYWI ENFIRFS 1:100 (oncogene 24p3)NEUTROPHIL GELATINASE- YATIYE RTFVPGC KYLGLPE ASSOCIATED LIPOCALIN;(125) Q (126) N (127) ONCOGENIC LIPOCALIN 24P3;lipocalin 2 (oncogene 24p3) S0092 paired box gene  7849PAX8; paired box gene 8; paired box DDSDQDSC RQHYPEA NTPLGRN 1:30- 8gene 8 isoform PAX8C; paired box RLSIDSQ YASPSHT LSTHQTY 1:100gene 8 isoform PAX8D; paired box (128) K (129) PVVADgene 8 isoform PAX8E; paired box (130) gene 8 isoform PAX8A; paired boxgene 8 isoform PAX8B; PAIRED DOMAIN GENE 8 PAX8/PPARG FUSION GENE S0093mesothelin 10232 CAK1; SMR; MSLN; mesothelin; RLVSCPGP KMSPEDI SPEELSS1:500 MEGAKARYOCYTE- LDQDQQE RKWNVTS VPPSSIW POTENTIATING FACTOR; (131)LETLK  AVRPQD  SOLUBLE MPF/MESOTHELIN- (132) (133)RELATED PROTEIN; mesothelin isoform 2 precursor; mesothelinisoform 1 precursor; megakaryocyte potentiating factor precursor;ANTIGEN RECOGNIZED BY MONOCLONAL ANTIBODY S0094 kallikrein 6   5653Bssp; PRSS18; KLK6; Klk7; SP59; EEQNKLVH ELIQPLP GKTADGD 1:150-(neurosin, zyme) PRSS9; MGC9355; protease M; GGPCDKTS LERDCSA FPDTIQC1:300 kallikrein 6 preproprotein; pro-  H (134) NT  (136)tease, serine, 18; protease,   (135) serine, 9; kallikrein 6 (neurosin, zyme) S0095 Rap guanine 10411 bcm910; MGC21410; REQWPERRKVNSAGD QQLKVID 1:250- nucleotide  9330170P05Rik; EPAC; RAPGEF3;RCHRLENG AIGLQPD NQRELSR 1:1000 exchange factor  cAMP-GEFI; RAP guanine-CGNA  AR  LSRELE (GEF) 3 nucleotide-exchange factor 3; (137) (139) (140)EXCHANGE PROTEIN ACTIVATED BY cAMP; RAPguanine-nucleotide-exchange factor (GEF) 3; cAMP-REGULATEDGUANINE NUCLEOTIDE EXCHANGE FACTOR I; RAP GUANINE NUCLE S0096 ATPase, H+525 Vma2; VPP3; ATP6V1B1; RTA1B; REHMQAV KKSKAVL DEFYSRE 1:100-transporting, 3.6.3.14; VATB; ATP6B1; V-ATPase TRNYITHPR DYHDDN GRLQDLA1:800 lysosomal 56/58  B1 subunit; H+-ATPase beta 1 (141) (142) PDTALkDa, V1   subunit; H(+)-transporting two- (143) subunit B, sector ATPase, 58 kD subunit;  isoform 1 (Renalvacuolar proton pump, subunit 3; tubular acidosis endomembrane proton pump 58 kDa with deafness) subunit; ATPase, H+transporting, lysos S0097 frizzled homolog 8325FZ-8; hFZ8; FZD8; frizzled 8;   KQQDGPTK ELRVLSK RRGGEGG 1:100-8 (Drosophila) frizzled homolog 8 (Drosophila);  THKLEKLM ANAIVPGEENPSAA 1:500 FRIZZLED, DROSOPHILA, HOMOLOG OF, 8 IR (144) LSGGE KGHLMG(145) (146) S0099 histone 1, H2ba 255626 HIST1H2BA; histone 1, H2baMPEVSSKG GFKKAVV KEGKKRK 1:333- ATISKK KTQK RTRKE 1:500 (147) (148)(149) S0110 hypothetical  84259 MGC2714; hypothetical protein RYAFDFARSVFYQYL EDGAWPV 1:500- protein MGC2714 DKDQRSLD EQSKYRV LLDEFVE 1:2500MGC2714 ID (150) MNKDQ WQKVRQ (151) TS  (152) S0117 reproduction 8 7993D8S2298E; REPS; reproduction 8; SFKSPQVY RKKQQEA EDIGITV 1:200-Reproduction/chromosome 8 LKEEEEKN QGEKASR DTVLILE 1:375 EKR (153) YIE EKEQTN  (154) (155) S0119 slit homolog 1 6585SLIT3; MEGF4; SLIL1; Slit-1; SLIT1;  KAFRGATD DFRCEEG DGTSFAE 1:900(Drosophila) slit homolog 1 (Drosophila); SLIT, LKNLRLDK QEEGGCL EVEKPTKDROSOPHILA, HOMOLOG OF, 1; NQ (156) PRPQ  CGCALCAMULTIPLE EPIDERMAL GROWTH (157) (158) FACTOR-LIKE DOMAINS 4 S0122leucyl-tRNA 23395 6.1.1.4; MGC26121; KIAA0028; QRIKEQAS HAKTKEK KSPQPQL1:150 synthetase 2, LEURS; LARS2; leucine translase; KISEADKS LEVTWEKLSNKEKA mitochondrial leucine-tRNA ligase; LEUCYL-tRNA KPKF  MSKSKHNEARK  SYNTHETASE, MITOCHONDRIAL; (159) (160) (161)leucyl-tRNA synthetase 2, mitochondrial; leucyl-tRNA synthetase 2, mitochondrial pre- cursor S0123 homeo box D4 3233HOX4B; HOXD4; HHO.C13; HOX- MLFEQGQQ KDQKAKG HSSQGRL 1:100-5.1; HOMEOBOX D4; HOMEOBOX ALELPECT ILHSPAS PEAPKLT 1:5004B; HOMEOBOX X; homeo box D4; (162) QSPERS HL homeobox protein Hox-D4; Hox-4.2, (163) (164)mouse, homolog of homeo box X S0124 sphingosine-1- 8879KIAA1252; SPL; SGPL1; KRGARRGG KIVRVPL QFLKDIR 1:990- phosphate lyase sphingosine-l-phosphate lyase 1 WKRKMPS TKMMEVD ESVTQIM 1:1500 1TDL (165) VR  KNPKA (166) (167) S0126 HBxAg trans- 55789XTP1; HBxAg transactivated protein  SKQGVVIL VQTFSRC LKKPFQP 1:450-activated 1 DDKSKELP ILCSKDE FQRTRSF 1:1600 protein 1 HW (168) VDLDELRM  (169) (170) S0132 SRY (sex  6662 SRA1; CMD1; CMPD1; SOX9; SRY-MNLLDPFM NTFPKGE KNGQAEA 1:100- determining  BOX 9; transcription factor SOX9; KMTDEQEK PDLKKES EEATEQT 1:500region Y)-box 9  SRY-RELATED HMG-BOX GENE GLS (171) EEDK  HISPN(campomelic 9; SEX REVERSAL, AUTOSOMAL, (172) (173) dysplasia, 1; SRY (sex-determining region Y)- autosomalbox 9 protein; SRY (sex-determining sex-reversal)region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal); SRY (S0137 cadherin, EGF  1952 Flamingo1; CELSR2; EGFL2; QASSLRLEP ELKGFAERSGKSQP 1:1800- LAG seven- KIAA0279; MEGF3; CDHF10; EGF- GRANDGD RLQRNESSYIPFLL 1:5000 pass G-type  like-domain, multiple 2; epidermal WH (174)GLDSGR REE  receptor 2  growth factor-like 2; multiple (175) (176)(flamingo  epidermal growth factor-like domains homolog,3; cadherin EGF LAG seven-pass G- Drosophila)type receptor 2; cadherin, EGF LAG seven-pass G-type receptor 2 S0139gamma-glutamyl 8836 3.4.19.9; GGH; gamma-glutamyl RRSDYAKV KNFTMNEEFFVNEA 1:2500- hydrolase  hydrolase precursor; gamma-glutamyl AKIFYNLSI KLKKFFN RKNNHHF 1:30000 (conjugase,  hydrolase (conjugase,QSFDD VLTTN KSESEE folylpoly- folylpolygammaglutamyl hydrolase) (177)(178) (179) gammagluta myl hydrolase) S0140 bullous  667BP240; FLJ13425; FLJ32235; KNTQAAEA QENQPEN KQMEKDL 1:250- pemphigoid  FLJ21489; FLJ30627; CATX-15; LVKLYETK SKTLATQ AFQKQVA 1:20000antigen 1,  KIAA0728; BPAG1; dystonin; LCE (180) LNQ  EKQLK 230/240 kDahemidesmosomal plaque protein; (181) (182) bullous pemphigoid antigen 1,230/240 kDa; bullous pemphigoid antigen 1 (230/240 kD); bullouspemphigoid antigen 1 isoform 1cA precursor; bullo S0143 fatty acid  21942.3.1.85; OA-519; FASN; MGC14367;  EFVEQLRK DRHPQAL REVRQLT 1:5000-synthase MGC15706; fatty acid synthase EGVFAKEV EAAQAEL LRKLQEL 1:30000R (183) QQHD SSKADE (184) (185) S0143 fatty acid  21942.3.1.85; OA-519; FASN; MGC14367;  REVRQLTL N/A N/A 1:200- P3 synthaseMGC15706; fatty acid synthase RKLQELSS 1:630 KADE (186) S0144 matrix4323 MMP-X1; 3.4.24.-; MMP14; AYIREGHE DEASLEP RGSFMGS 1:500-metallopro-  MTMMP1; MT1-MMP ; membrane- KQADIMIFF GYPKHIK DEVFTYF1:20000 teinase 14 type-1 matrix metalloproteinase; AE (187) ELGR  YK (membrane- matrix metalloproteinase 14 (188) (189) inserted)preproprotein; MATRIX METALLOPROTEINASE 14, MEMBRANE-TYPE; matrixmetalloproteinase 14 (membrane- inserted); membrane-type matrixmetalloprotein S0147 cystatin A   1475 STF1; CSTA; STFA; cystatin AS;MIPGGLSE NETYGKL DLVLTGY 1:100- (stefin A) cystatin A (stefin A)AKPATPEIQ EAVQYKT QVDKNKD 1:5000 EIV (190) Q (191) DELTGF (192) S0149transient  55503 TRPV6; ECAC2; CAT1; CATL; RQEHCMSE QGHKWG RACGKRV1:400- receptor CALCIUM TRANSPORTER 1; HFKNRPAC ESPSQGT SEGDRNG 1:20000potential cation CALCIUM TRANSPORTER-LIKE LGAR  QAGAGK SGGGKW channel,PROTEIN; EPITHELIAL CALCIUM (193) (194) G (195) subfamilyCHANNEL 2; transient receptor V, member 6potential cation channel, subfamily  V, member 6 S0156 fatty acid  2173B-FABP; FABP7; FABPB; MRG; MVEAFCAT QVGNVTK KVVIRTL 1:100- binding mammary-derived growth inhibitor- WKLTNSQN PTVIISQ STFKNTE 1:20000protein related; FATTY ACID-BINDING (196) E (197) (198) 7, brainPROTEIN 7; FATTY ACID- BINDING PROTEIN, BRAIN; fattyacid binding protein 7, brain S0158 cadherin 3, type 1001CDHP; HJMD; PCAD; CDH3; RAVFREAE QEPALFS QKYEAHV 1:150- 1, P-cadherin placental cadherin; CADHERIN, VTLEAGGA DTNDDFT PENAVGH 1:2000(placental) PLACENTAL; cadherin 3, P-cadherin   EQE  VRN  E (201)(placental); calcium- (199) (200) dependent adhesion protein, placental; cadherin  3, type 1   preproprotein; cadherin 3,type 1, P-cadherin (placental) S0165 chemokine (C-X-C 2919MGSA-a; NAP-3; CXCL1; SCYB1; KKIIEKML N/A N/A 1:100- motif) ligand 1GROa; GRO1, FORMERLY; GRO NSDKSN 1:500 (melanoma growthPROTEIN, ALPHA; GRO1 (202) stimulating  ONCOGENE, FORMERLY;activity, alpha) MELANOMA GROWTH STIMULATORY ACTIVITY,ALPHA; GRO1 oncogene (melanoma growth-stimulating activity);CHEMOKINE, CXC MOTIF, LIGAND 1; GRO1 oncogene (melanoma grow S0171baculoviral IAP null BIRC5; baculoviral IAP repeat- GKPGNQNS QAEAPLVNCFLTER 1:22500- repeat-  containing 5 (survivin) KNEPPKKR PLSRQNKKAQPDE 1:30000 containing ERER  (204) (205) 5 (survivin) (203) S0193procollagen-  5352 PLOD2; LYSYL HYDROXYLASE 2; EFDTVDLS NKEVYHE KQVDLEN1:20000 lysine,  LYSINE HYDROXYLASE 2; AVDVHPN KDIKVFF VWLDFIR2-oxoglutarate  PROCOLLAGEN-LYSINE, 2- (206) DKAK  E (208) 5-dioxygenaseOXOGLUTARATE 5- (207) (lysine DIOXYGENASE 2; procollagen- hydroxylase) 2lysine, 2-oxoglutarate 5-dioxygenase(lysine hydroxylase) 2; procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2 isoformS0202 PTK7 protein  5754 PTK7; CCK4; protein-tyrosine kinase LKKPQDSQKAKRLQK KDRPSFS 1:500- tyrosine kinase  PTK7; colon carcinoma kinase-4;LEEGKPGY QPEGEEP EIASALG 1:800 7 PTK7 protein tyrosine kinase 7; PTK7LD (209) EME  DSTVDSK protein tyrosine kinase 7 isoform e (210) P (211)precursor; PTK7 protein tyrosine kinase 7 isoform a precursor; PTK7protein tyrosine kinase 7 isoform d precursor; S0211 cytochrome P450,1549 CYPIIA7; P450-IIA4; 1.14.14.1; KRGIEERIQ DRVIGKN NPQHFLD 1:500-family 2,  CPA7; CYP2A7; CPAD; EESGFLIE RQPKFED DKGQFKK 1:2500subfamily A,  CYTOCHROME P450, SUBFAMILY (212) RTK  SD  polypeptide 7IIA, POLYPEPTIDE 7; cytochrome (213) (214)P450, subfamily IIA (phenobarbital- inducible), polypeptide 7; cyto-chrome P450, family 2, subfamily A, polypeptide 7; cytochrome P450,family 2, su S0218 solute carrier  222962SLC29A4; solute carrier family 29 RHCILGEW KQRELAG RNAHGSC 1:20-family 29  (nucleoside transporters), member 4 LPILIMAVF NTMTVSY LHASTAN1:50 (nucleoside N (215) MS  GSILAGL transporters), (216) (217) member 4S0221 solute carrier  9153 HCNT2; SLC28A2; HsT17153; ELMEKEVE KARSFCKKNKRLSG 1:500- family 28  SPNT1; CONCENTRATIVE PEGSKRTD THARLFK MEEWIEG1:1200 (sodium-coupled NUCLEOSIDE TRANSPORTER 2; (218) K (219) EK nucleoside  SODIUM-DEPENDENT PURINE (220) transporter),NUCLEOSIDE TRANSPORTER 1; member 2 solute carrier family 28 (sodium-coupled nucleoside transporter), member 2 S0223 angiopoietin- 51129HFARP; FIAF; ANGPTL4; PGAR; EGSTDLPL KVAQQQR DHKHLDH 1:30- like 4angiopoietin-like 4; FASTING- APESRVDP HLEKQHL EVAKPAR 1:10000INDUCED ADIPOSE FACTOR; E (221) R (222) RKRLPEPPARG ANGIOPOIETIN-RELATED (223) PROTEIN; HEPATICFIBRINOGEN/ANGIOPOIETIN- RELATED PROTEIN S0235 carcinoembryonic 1048CEACAM5; CD66e; KLTIESTPF KSDLVNE KPVEDKD 1:500- antigen-related carcinoembryonic antigen-related   NVAEGKEC EATGQFR AVAFTCE 1:4500cell adhesion  cell adhesion molecule 5 (224) VYPELPK PEAQ  molecule 5(225) (226) S0237 podocalyxin-like 5420 podocalyxin-like; Gp200; PCLP;DEKLISLIC KDKWDEL DSWIVPL 1:1000- PODXL; PODOCALYXIN-LIKE RAVKATFNKEAGVSD DNLTKDD 1:2000 PROTEIN; podocalyxin-like precursor PAQDK MKLGDLDEEEDT (227) (228) HL  (229) S0238 xenotropic and 9213X3; XPR1; X RECEPTOR; SYG1, EAVVTNEL RRYRDTK KARDTKV 1:100- polytropic YEAST, HOMOLOG OF; xenotropic EDGDRQKA RAFPHLV LIEDTDD 1:500 retrovirusand polytropic retrovirus receptor MKRLR NAGK EANT  receptor (230) (231)(232) S0241 glycyl-tRNA 2617 GlyRS; GARS; CMT2D; 6.1.1.14; RKRVLEAKRHGVSHK EARYPLF 1:500- synthetase SMAD1; GLYCYL-tRNA ELALQPKD VDDSSGSEGQETGK 1:7500 SYNTHETASE; glycine tRNA ligase; DIVD  IGRRYAR KETIEECharcot-Marie-Tooth neuropathy, (233) (234) (235) neuronal type, D S0244dachshund  1602 DACH1; FLJ10138; dachshund DLAGHDM EKQVQLE EADRSGG1:100- homolog 1 homolog (Drosophila); GHESKRMH KTELKMD RTDAERT 1:3000(Drosophila) DACHSHUND, DROSOPHILA, IEKDE  FLRERE IQDGRHOMOLOG OF; dachshund homolog (236) (237) (238)1 (Drosophila); dachshund homolog 1 isoform a; dachshund homolog 1isoform b; dachshund homolog 1 isoform c S0251 transcription  29841TFCP2L2; LBP-32; MGR; GRHL1; EALYPQRR DYYKVPR DKYDVPH 1:5400 factormammalian grainyhead; LBP protein SYTSEDEA ERRSSTA DKIGKIF CP2-like 232; transcription factor CP2-like 2; WK (239) KPEVE KKCKKleader-binding protein 32 isoform 2; (240) (241)leader-binding protein 32 isoform 1 S0253 lysosomal  55353LAPTM4B; lysosomal associated DPDQYNFS EYIRQLP DTTVLLP 1:500-associated pro- protein transmembrane 4 beta SSELGGDF PNFPYRD PYDDATV1:2000 tein trans-  EFMDD D (243) NGAAKE membrane 4  (242) (244) betaS0255 cyclin E2 9134 CYCE2; CCNE2; cyclin E2; Gl/S- RREEVTKK KESRYVHDFFDRFM 1:1000- specific cyclin E2; cyclin E2   HQYEIR DKHFEVL LTQKDIN1:2000 isoform 2; cyclin E2 isoform 3;  (245) HSDLE K (247)cyclin E2 isoform 1 (246) S0260 nicastrin 23385KIAA0253; nicastrin; NCSTN; APH2; ESKHFTRD ETDRLPR ESRWKDI 1:2400-ANTERIOR PHARYNX LMEKLKGR CVRSTAR RARIFLI 1:5400DEFECTIVE 2, C. ELEGANS, TSR (248) LAR  ASKELE HOMOLOG OF (249) (250)S0265 FXYD domain 5349 MAT-8; MAT8; PLML; FXYD3; KVTLGLLV SEWRSSGKCKCKFG 1:400- containing ion phospholemman-like protein; FLAGFPVL EQAGRQKSGHHP 1:1200 transport  MAMMARY TUMOR, 8-1(D; FXYD DANDLED (252) GE regulator 3 domain-containing ion transport (251) (253)regulator 3; FXYD domain containing ion transport regulator 3; FXYDdomain containing ion transport regulator 3 isoform 2 precursor; FXYD domai S0267 immunoglobulin 3321 EWI-3; V8; IGSF3; immunoglobinKVAKESDS EREKTVT KRAEDTA 1:200- superfamily,  superfamily, member 3;VFVLKIYH GEFIDKE GQTALTV 1:250 member 3immunoglobulin superfamily, member LRQED SKRPK  MRPD 3 (254) (255) (256)S0270 signal trans-  10254 STAM2B; STAM2; DKFZp564C047; KVARKVR ETEVAAVEIKKSEP 1:1000- ducing adaptor  Hbp; STAM2A; SIGNAL- ALYDFEAV DKLNVIDEPVYIDE 1:9000 molecule (SH3  TRANSDUCING ADAPTOR EDNE  DDVE DKMDRdomain and ITAM  MOLECULE 2; signal transducing (257) (258) (259)motif) 2 adaptor molecule 2; STAM-like protein containing SH3 and ITAMdomains 2; signal transducing  adaptor molecule (SH3 domain and ITAM motif) 2 S0273 dickkopf homolog 22943DKK1; DKK-1; SK; dickkopf-1 like; DEECGTDE RGEIEET N/A 1:400- 1  dickkopf (Xenopus laevis) homolog 1; YCASPTRG ITESFGN 1:500(Xenopus laevis) dickkopf homolog 1 (Xenopus laevis);  GD (260) DHSTLDDICKKOPF, XENOPUS, HOMOLOG (261) OF, 1 S0280 solute carrier  65010SLC26A6; solute carrier family 26, MDLRRRD DTDIYRD EFYSDAL 1:1800-family 26,  member 6 YHMERPLL VAEYSEA KQRCGVD 1:2400 member 6 NQEHLEEKE  VDFLISQ (262) (263) KKK  (264) S0286 WNT inhibitory  11197WIF1; WIF-1; WNT inhibitory factor DAHQARVL ERRICEC KRYEASL 1:90factor 1 1; Wnt inhibitory factor-1 precursor IGFEEDIL PDGFHGP IHALRPAIVSE  HCEK  GAQLR (265) (266) (267) S0288 preferentially 23532MAPE; PRAME; OPA- KRKVDGLS KEGACDE DIKMILK 1:1200 expressed  INTERACTING PROTEIN 4; Opa- TEAEQPFIP LFSYLIE MVQLDSI antigeninteracting protein OIP4;   VE (268) KVKRKK EDLE  in melanomapreferentially expressed antigen  (269) (270)in melanoma; melanoma antigen  preferentially expressed in tumors S0295prostaglandin E 9536 PGES; TP53112; MGST1L1; PP1294; RLRKKAFA RSDPDVERVAHTVA 1:100- synthase PP102; PTGES; MGC10317; PIG12; NPEDALR RCLRAHRYLGKLRA 1:2400 MGST1-Ll; MGST-IV; MGST1-like (271) ND  PIR 1; p53-INDUCED GENE 12; (272) (273) prostaglandin E synthase; p53-induced apoptosis protein  12; prostaglandin E synthaseisoform 2; prostaglandin E synthase isoform 1; micros S0296solute carrier 8140 SLC7A5; MPE16; D16S469E; CD98; KRRALAAP EAREKMLMIWLRHR 1:300- family 7  LAT1; 4F2 light chain; Membrane AAEEKEEAAAKSADG KPELERP 1:5000 (cationic amino protein E16; L-TYPE AMINO ACIDR (274) SAPAGE IK  acid  TRANSPORTER 1; Solute carrier (275) (276)transporter, family 7, member 5; solute carrier y+ system),family 7 (cationic amino acid member 5 transporter, y+ system), member 5S0296 solute carrier 8140 SLC7A5; MPE16; D16S469E; CD98; KRRALAAP N/AN/A 1:225- P1 family 7  LAT1; 4F2 light chain; Membrane AAEEKEEA 1:3150(cationic amino protein E16; L-TYPE AMINO ACID R (277) acid  TRANSPORTER 1; Solute carrier transporter,family 7, member 5; solute carrier y+ system),family 7 (cationic amino acid member 5 transporter, y+ system), member 5S0297 v-maf 7975 FLJ32205; NFE2U; MAFK; NFE2, KPNKALKV KRVTQKE RLELDAL1:333- musculoapo- 18-KD SUBUNIT; nuclear factor KKEAGE ELERQRV RSKYE1:800 neurotic erythroid-2, ubiquitous (p18); (278) ELQQEVE (280)fibrosarcoma  NUCLEAR FACTOR ERYTHROID K (279) oncogene homolog2, UBIQUITOUS SUBUNIT; v-maf K (avian) musculoaponeurotic fibrosarcomaoncogene homolog K (avian); v-maf avian musculoaponeuroticfibrosarcoma oncogen S0301 signal peptide,  57758SCUBE2; signal peptide, CUB KMHTDGRS KKGFKLL KRTEKRL 1:3500-CUB domain,  domain, EGF-like 2 CLEREDTV TDEKSCQ RKAIRTL 1:5400EGF-like 2 LEVTE  DVDE RKAVHRE (281) (282) (283) S0303 gamma-amino- 2564GABRE; GABA-A RECEPTOR, RVEGPQTE EETKSTE KWENFKL 1:300- butyric acid EPSILON POLYPEPTIDE; GAMMA- SKNEASSR TETGSRV EINEKNS 1:500 (GABA) A  AMINOBUTYRIC ACID D (284) GKLPE  WKLFQFD receptor,RECEPTOR, EPSILON; gamma- (285) (286) epsilonaminobutyric acid (GABA) A receptor, epsilon; gamma-aminobutyric acid(GABA) A receptor, epsilon isoform 2; gamma-aminobutyric acid (GABA) Areceptor, epsilon is S0305 S100 calcium  6281CAL1L; GP11; p10; 42C; S100A10; DKGYLTKE KDPLAVD N/A 1:8332-binding protein ANX2LG; CLP11; Ca[1]; DLRVLMEK KIMKDLD 1:24996A10 (annexin II CALPACTIN I, p11 SUBUNIT; E (287) QCRDGK ligand,  ANNEXIN II, LIGHT CHAIN; (288) calpactin  CALPACTIN I, LIGHT CHAIN; S100 I, lightcalcium-binding protein A10 (annexin polypeptideII ligand, calpactin I, light  (p11)) polypeptide (p11)); S100 calcium binding protein A10 S0311 v-myb myelo- 4605 MYBL2; MGC15600; MYB-MSRRTRCE EEDLKEV RRSPIKK 1:750- blastosis viral  RELATED GENE BMYB; MYB-DLDELHYQ LRSEAGI VRKSLAL 1:5000 oncogene homologrelated protein B; v-myb DTDSD ELIIEDD DIVDED (avian)-like2myeloblastosis viral oncogene (289) IR (291)homolog (avian)-like 2; V-MYB (290) AVIAN MYELOBLASTOSIS VIRALONCOGENE HOMOLOG-LIKE 2 S0312 nucleoside 4860 NP; 2.4.2.1; nucleoside  EDYKNTAE DERFGDR KVIMDYE 1:1000- phosphorylase phosphorylase; PURINE-WLLSHTKH FPAMSDA SLEKANH 1:3600 NUCLEOSIDE: ORTHOPHOSPHATE R (292)YDRTMRQ EE  RIBOSYLTRANSFERASE; purine R (293) (294)nucleoside phosphorylase; PNP NUCLEOSIDE PHOSPHORYLASEDEFICIENCY; ATAXIA WITH DEFICIENT CELLULAR IMMUNITY S0314 chaperonin 22948 KIAA0098; CCT5; chaperonin DQDRKSRL KGVIVDK RMILKID 1:6000-containing   containing TCP1, subunit 5 (epsilon) MGLEALKS DFSHPQMDIRKPG 1:30000 TCP1, subunit  HIMAAK PKKVED ESEE  5 (epsilon) (295)(296) (297) S0315 non-metastatic   4830 GAAD; NME1; NDPKA; 2.7.4.6;RLQPEFKP KFMQASE DSVESAE 1:9000- cells 1,  NM23-H1; AWD NM23H1B; GZMA-KQLEGTMA DLLKEHY KEIGLWF 1:18000 protein (NM23A)ACTIVATED DNase; NUCLEOSIDE NCER  VDLKDR HPEELVD expressed inDIPHOSPHATE KINASE-A; AWD, (298) (299) (300) DROSOPHILA, HOMOLOG OF;METASTASIS INHIBITION FACTOR NM23; nucleoside-diphosphate kinase 1 isoform b; NONMETASTATIC PROTEIN 23,HOMOLOG 1; nucleo S0316 squalene  6713SQLE; 1.14.99.7; squalene epoxidase; KSPPESENK RDGRKVT DHLKEPF 1:1000-epoxidase squalene monooxygenase EQLEARRR VIERDLK LEATDNS 1:10000R (301) EPDR  HLR  (302) (303) S0319 pregnancy- 29948OKL38; pregnancy-induced growth DLEVKDW EYHKVHQ RHQLLCF 1:900 inducedinhibitor; PREGNANCY-INDUCED MQKKRRG MMREQSI KEDCQAV growth GROWTH INHIBITOR OKL38 LRNSR  LSPSPYE FQDLEGV inhibitor (304) GYR  EK (305) (306) S0326 mal, T-cell 114569 MAL2; mal, T-cell differentiationGPDILRTYS CSLGLAL N/A 1:120- differentiation  protein 2 GAFVCLE RRWRP1:1200 protein 2 (307) (308) S0330 aldo-keto  16451.1.1.213; 2-ALPHA-HSD; 1.3.1.20; RYLTLDIFA N/A N/A 1:2500-reductase family 20-ALPHA-HSD; MGC8954; H-37; GPPNYPFS 1:750001, member C1/2  HAKRC; MBAB; C9; DDH1; DEY (309) (dihydrodiol AKR1C1; trans-1,2-dihydrobenzene- dehydrogenase 1,2-diol dehydrogenase; chlordecone 1; 20-alphareductase homolog; aldo-keto (3-alpha)-reductase C; 20 alpha-hydroxysteroid hydroxysteroiddehydrogenase; hepatic dihydrodiol dehydrogenase) S0330- aldo-keto  16451.1.1.213; 2-ALPHA-HSD; 1.3.1.20;  RYLTLDIFA N/A N/A 1:600 x1reductase family 20-ALPHA-HSD; MGC8954; H-37; GPPNYPFS 1, memberC1/2 HAKRC; MBAB; C9; DDH1; DEY (310) (dihydrodiol AKR1C1; trans-1,2-dihydrobenzene- dehydrogenase 1,2-diol dehydrogenase; chlordecone 1; 20-alpha reductase homolog; aldo-keto (3-alpha)-reductase C; 20 alpha-hydroxysteroid hydroxysteroiddehydrogenase; hepatic dihydrodiol dehydrogenase) S0331 aldo-keto  8644HA1753; 1.1.1.188; DD3; h1uPGFS; HYFNSDSF N/A N/A 1:300-reductase family HSD17B5; 1.3.1.20; 1.1.1.213; ASHPNYPY 1:999 1, memberAKR1C3; KIAA0119; HAKRB; SDEY (311) C3 (3-alphaHAKRe; trans-1,2-dihydrobenzene- hydroxysteroid1,2-diol dehydrogenase; chlordecone dehydrogenase, reductase homolog; dihydrodiol type II) dehydrogenase 3; prostaglandin Fsynthase; ALDO-KETO REDUCTASE B; 3- S0331- aldo-keto  8644HA1753; 1.1.1.188; DD3; h1uPGFS; HYFNSDSF N/A N/A 1:150- x1reductase family HSD17B5; 1.3.1.20; 1.1.1.213; ASHPNYPY 1:3001, member C3 AKR1C3; KIAA0119; HAKRB; SDEY (312) (3-alpha HAKRe; trans-1,2-dihydrobenzene- hydroxysteroid1,2-diol dehydrogenase; chlordecone dehydrogenase,reductase homolog; dihydrodiol type II) dehydrogenase 3; prostaglandin Fsynthase; ALDO-KETO REDUCTASE B; 3- S0332 aldo-keto  16451.1.1.213; 2-ALPHA-HSD; 1.3.1.20; RYVVMDFL N/A N/A 1:300-reductase family 20-ALPHA-HSD; MGC8954; H-37; MDHPDYPF 1:4001, member C4 HAKRC; MBAB; C9; DDH1; SDEY (313) (dihydrodiol AKR1C1; trans-1,2-dihydrobenzene- dehydrogenase1,2-diol dehydrogenase; chlordecone 1; 20- reductase homolog; aldo-ketoalpha (3-alpha)- reductase C; 20 alpha-hydroxysteroid hydroxysteroiddehydrogenase; hepatic dihydrodiol dehydrogenase) S0332- aldo-keto  16451.1.1.213; 2-ALPHA-HSD; 1.3.1.20; RYVVMDFL N/A N/A 1:75- x1reductase family 20-ALPHA-HSD; MGC8954; H-37; MDHPDYPF 1:1501, member C4 HAKRC; MBAB; C9; DDH1; SDEY (314) (dihydrodiol AKR1C1; trans-1,2-dihydrobenzene- dehydrogenase 1,2-diol dehydrogenase; chlordecone 1; 20- reductase homolog; aldo-ketoalpha (3-alpha)- reductase C; 20 alpha-hydroxysteroid hydroxysteroiddehydrogenase; hepatic dihydrodiol dehydrogenase) S0336 chromosome 20 140809 C20orf139; chromosome 20 open DPAKVQSL RETIPAK N/A 1:1600-open reading  reading frame 139 VDTIREDP LVQSTLS 1:2400 frame 139D (315) DLR  (316) S0342 solute carrier 154091SLC2Al2; solute carrier family 2 SDTTEELT N/A N/A 1:400- family 2 (facilitated glucose transporter), VIKSSLKDE 1:1250 (facilitated member 12 (317) glucose transporter), member 12 S0343 solute carrier154091 SLC2Al2; solute carrier family 2 HSRSSLMP N/A N/A 1:50-family 2   (facilitated glucose transporter), LRNDVDKR 1:125(facilitated  member 12 (318) glucose transporter), member 12 S0357HTPAP protein 84513 HTPAP; HTPAP protein YRNPYVEA N/A N/A 1:100-EYFPTKPM 1:300 FVIA (319) S0364 KIAA0746 protein 23231KIAA0746; KIAA0746 protein KKFPRFRN N/A N/A 1:200- RELEATRR 1:300QRMD (320) S0367 peroxisomal  122970 PTE2B; peroxisomal acyl-CoASGNTAINY N/A N/A 1:200- acyl-  thioesterase 2B KHSSIP 1:600CoAthioesterase (321) 2B S0374 chloride  53405CLIC5; chloride intracellular   DANTCGED N/A N/A 1:5000- intracellularchannel 5 KGSRRKFL 1:9000 channel 5 DGDE (322) S0380 keratinocyte 200634KRTCAP3; keratinocyte associated QLEEMTEL N/A N/A 1:2000- associated  protein 3 ESPKCKRQ 1:9000 protein 3 ENEQ (323) S0384 FERM, RhoGEF 10160p63RhoGEF; CDEP; FARP1; QADGAASA N/A N/A 1:100 (ARHGEF) andchondrocyte-derived ezrin-like   PTEEEEEV pleckstrin protein; FERM, RhoGEF, and  VKDR  domain protein pleckstrin domain protein 1; FERM,  (324) 1 (chondrocyte-ARHGEF, AND PLECKSTRIN DOMAIN- derived) CONTAINING PROTEIN 1; FERM,RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte- derived)S0388 trichorhino- 7227 GC79; TRPS1; TRPS1 GENE; SGDSLETK N/A N/A 1:600phalangeal trichorhinophalangeal syndrome 1;  EDQKMSPK syndrome Izinc finger transcription factor  ATEE  TRPS1 (325) S0396cytochrome P450, 1576 1.14.14.1; HLP; CYP3A3; CYP3A4; RKSVKRM N/A N/A1:15 family 3,  P450C3; NF-25; CP33; CP34; P450- KESRLEDT subfamily A,III, STEROID-INDUCIBLE; QKHRV polypeptide 4nifedipine oxidase; glucocorticoid- (326) inducible P450; CYTOCHROMEP450PCN1; P450, FAMILY III; P450- III, steroid inducible; cytochromeP450, subfamily IIIA, polypeptide 4; S0398 FAT tumor  2195CDHF7; FAT; cadherin ME5; FAT KIRLPEREK N/A N/A 1:45- suppressortumor suppressor precursor;  PDRERNAR 1:200 homolog 1cadherin-related tumor suppressor  REP (327) (Drosophila)homolog precursor; cadherin family  member 7 precursor; homolog of Drosophila Fat protein precursor;  FAT tumor suppressor homolog 1 (Drosophila); FAT TUMOR SUPPRESS S0401 granulin 2896ACROGRANIN; PROEPITHELIN; RGTKCLRR N/A N/A 1:600-PROGRANULIN; PEPI; PCDGF; EAPRWDAP 1:3000 granulin; GRN; EPITHELIN LRDP PRECURSOR (328) S0404 N-myc downstream 10397 HMSNL; TARG1; CMT4D; RTP;GTRSRSHT N/A N/A 1:100- regulated gene 1 PROXY1; NDRG1; GC4; NMSL;SEGTRSRS 1:900 TDDS; RIT42; NDR1; differentiation- HTSE related gene 1 protein; nickel- (329) specific induction protein Cap43; protein regulated by oxygen-1; NMYC DOWNSTREAM-REGULATEDGENE 1; reducing agents and tunicamycin-respon S0411 fatty acid  2171PAFABP; EFABP; E-FABP; FABP5; EETTADGR N/A N/A 1:1800 binding proteinPA-FABP; FATTY ACID-BINDING KTQTVCNF 5 (psoriasis-PROTEIN, EPIDERMAL; FATTY TD (330) associated) ACID-BINDING PROTEIN 5;FATTY ACID-BINDING PROTEIN, PSORIASIS-ASSOCIATED; fattyacid binding protein 5 (psoriasis- associated) S0413 cyclin-dependent1028 WBS; p57(KIP2); BWCR; CDKN1C; AKRKRSAP N/A N/A 1:2700kinase inhibitor BWS; Beckwith-Wiedemann EKSSGDVP 1C (p57, Kip2)syndrome; cyclin-dependent kinase  (331) inhibitor 1C (p57, Kip2) S0414alpha- 23600 AMACR; 5.1.99.4; ALPHA- RVDRPGSR N/A N/A 1:100 methylacyl-METHYLACYL-CoA RACEMASE; YDVSRLGR CoA racemase AMACR DEFICIENCY; AMACRGKRS  ALPHA-METHYLACYL-CoA (332) RACEMASE DEFICIENCY; alpha-methylacyl-CoA racemase isoform 1; alpha-methylacyl-CoA racemaseisoform 2 S0415 gamma-amino- 2562 MGC9051; GABRB3; GABA-A ETVDKLLK N/AN/A 1:600- butyric RECEPTOR, BETA-3 GYDIRLRP 1:1800 acid (GABA) APOLYPEPTIDE; GAMMA- D (333) receptor, beta  AMINOBUTYRIC ACID 3RECEPTOR, BETA-3; gamma- aminobutyric acid (GABA) A receptor,beta 3; gamma-aminobutyric acid (GABA) A receptor, beta 3 isoform 2precursor; gamma-aminobutyric acid (GABA) A rece S0417 HSV-1  22879HSRG1; KIAA0872; HSV-1 APGGAEDL N/A N/A 1:9000 stimulation-stimulation-related 1; HSV-1 EDTQFPSEE related gene 1stimulation-related gene 1 ARE (334) S0425 tumor necrosis  27242TNFRSF21; DR6; BM-018; TNFR- RKSSRTLK N/A N/A 1:9000 factor receptor related death receptor 6; tumor KGPRQDPS superfamily,necrosis factor receptor super- AIVE (335) member 21family, member 21; tumor necrosis  factor receptor superfamily, member 21 precursor S0429 jumonji domain 221037JMJD1C; TRIPS; jumonji domain GSESGDSD N/A N/A 1:1200 containing 1Ccontaining 1C; THYROID ESESKSEQR HORMONE RECEPTOR TKR (336) INTERACTOR 8S0432 chromosome 9  null C9orf140; chromosome 9 open reading EADSGDARN/A N/A 1:90- open reading  frame 140 RLPRARGE 1:300 frame 140RRRH (337) S0440 cell division  994 3.1.3.48; CDC25B; cell division RLERPQDR N/A N/A 1:350- cycle 25B cycle 25B; cell division cycle  DTPVQNKR 1:3600 25B isoform 4; cell division cycle   RRS (338)25B isoform 5; cell division cycle 25B isoform 1; cell division cycle 25B isoform 2;  cell division cycle 25B isoform 3S0445 laminin, beta 1 3912 LAMB1; LAMININ, BETA-1; CUTIS DRVEDVM N/A N/A1:600- LAXA-MARFANOID SYNDROME; MERESQFK 1:1800laminin, beta 1; laminin, beta 1 EKQE (339) precursor; LAMB1 NEONATALCUTIS LAXA WITH MARFANOID PHENOTYPE S0447 papillary renal  5546TPRC; MGC17178; MGC4723; DEAFKRLQ N/A N/A 1:4000- cell carcinomaPRCC; proline-rich protein PRCC; GKRNRGRE 1:6000 (translocation-RCCP1 PRCC/TFE3 FUSION GENE; E (340) associated)papillary renal cell carcinoma (translocation-associated); RENALCELL CARCINOMA, PAPILLARY, 1 GENE; papillary renal cellcarcinoma translocation-associated gene product S0455 tumor necrosis 8743 APO2L; TL2; Apo-2L; TNFSF10; RFQEEIKEN N/A N/A 1:900factor (ligand)  Apo-2 ligand; APO2 LIGAND; TNF- TKNDKQ superfamily,RELATED APOPTOSIS-INDUCING (341) member 10 LIGAND; TNF-related apoptosisinducing ligand TRAIL; tumor necrosis factor (ligand) super-family, member 10; TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY, MEMBER 10S0459 titin 7273 connectin; TMD; titin; CMD1G; KRDKEGVR N/A N/A 1:2700-CMPD4; TTN; F1132040; CMH9, WTKCNKK 1:8100included; titin isoform N2-A; titin  TLTD (342)isoform N2-B; titin isoform novex-1;titin isoform novex-2; titin isoform novex-3; cardiomyopathy, dilated 1G(autosomal dominant); TTN CARDIOMYOPATHY, FAMILIAL S0469 DNA  1676DFF45; DFF1; DFFA; ICAD; DFF-45; KEGSLLSK N/A N/A 1:600 fragmentation INHIBITOR OF CASPASE- QEESKAAF factor, 45 kDa, ACTIVATED DNase; DNAGEE (343) alpha  FRAGMENTATION FACTOR, 45- polypeptideKD, ALPHA SUBUNIT; DNA fragmentation factor, 45 kDa, alphapolypeptide; DNA fragmentation factor, 45 kD, alpha subunit; DNAfragmentation factor, 45 kD, alp S0494 caspase 2,  835ICH-1L/1S; CASP2; ICH1; CASP-2; ESDAGKEK N/A N/A 1:2000 apoptosis-ICH-1 protease; caspase 2 isoform 3; LPKMRLPT related caspase 2 isoform 4; NEDD2 apoptosis RSD (344) cysteine pro- regulatory gene; caspase 2 isoform 2 tease (neuralprecursor; caspase 2 isoform 1 precursor cell preproprotein; NEURALexpressed, PRECURSOR CELL EXPRESSED, developmentally DEVELOPMENTALLYdown-regulated DOWNREGULATED 2; 2) S0501 G1 to S phase 2935GSPT1; eRF3a; ETF3A; GST1, ERDKGKTV N/A N/A 1:15000 transition 1YEAST, HOMOLOG OF; PEPTIDE EVGRAYFE CHAIN RELEASE FACTOR 3A; G1-TEK (345) TO S-PHASE TRANSITION 1; G1 to S phase transition 1 S0502GCN5 general  2648 hGCN5; GCN5L2; GCN5 (general EKFRVEKD N/A N/A 1:9000control of  control of amino-acid synthesis,   KLVPEKR amino-acid yeast, homolog)-like 2; GCN5 general (346) synthesis 5-control of amino-acid synthesis 5- like 2 (yeast)like 2 (yeast); General control of amino acid synthesis, yeast, homolog- like 2 S0503 geminin, DNA 51053GMNN; geminin, DNA replication EVAEKRRK N/A N/A 1:333 replication inhibitor ALYEALKE inhibitor NEK (347) S0507 ADP- 64225ARL6IP2; ADP-ribosylation factor- ENYEDDDL N/A N/A 1:8000- ribosylationlike 6 interacting protein 2 VNSDEVM 1:9000 factor-like 6  KKP (348)interacting protein 2 S0511 DNA replication 51659Pfs2; DNA replication complex GINS PKADEIRTL N/A N/A 1:2000 complex GINSprotein PSF2 VKDMWDT protein PSF2 R (349) S0524 ankyrin repeat  55608ANKRD10; ankyrin repeat domain 10 RKRCLEDS N/A N/A 1:4500 domain 10EDFGVKKA RTE (350) S0527 potassium  null KCTD2; potassium channelEPKSFLCRL N/A N/A 1:900- channel tetramerisation domain containing 2CCQEDPEL 1:1500 tetramerisation  DS (351) domain  containing 2 S0528rabconnectin-3 23312 RC3; KIAA0856; rabconnectin-3 EEYDRESK N/A N/A1:350- SSDDVDYR 1:1200 GS (352) S0538 acidic  81611ANP32E; acidic (leucine-rich)   CVNGEIEG N/A N/A 1:1200 (leucine-nuclear phosphoprotein 32 family,  LNDTFKEL rich) nuclear member EEF (353) phosphoprotein  32 family,  member E S0544 chromosome 9  84904C9orf100; chromosome 9 open reading EQRARWER N/A N/A 1:40- open reading frame 100 KRACTARE 1:240 frame 100 (354) S0545 HpaII tiny  27037D22S1733E; HTF9C; HpaII tiny ERKQLECE N/A N/A 1:900- fragmentsfragments locus 9C; HpaII tiny QVLQKLAK 1:5400 locus 9Cfragments locus 9C isoform2; HpaII E (355)tiny fragments locus 9C isoform 1 S0546 cell division  157313CDCA2; cell division cycle  RNSETKVR N/A N/A 1:1200 cycle associated 2RSTRLQKD associated 2 LEN (356) S0553 mitotic 129401MP44; NUP35; LOC129401; SDYQVISD N/A N/A 1:3000- phosphoprotein NUCLEOPORIN, 35-1(D; mitotic RQTPKKDE 1:5400 44 phosphoprotein 44 (357)S0557 SMC4 structural 10051 SMC4L1; CAPC; hCAP-C; DIEGKLPQT N/A N/A1:200 maintenance of chromosome-associated polypeptide C; EQELKEchromosomes 4- SMC4 (structural maintenance of (358) like 1 (yeast)chromosomes 4, yeast)-like 1; SMC4 structural maintenance ofchromosomes 4-like 1 (yeast); structural maintenance ofchromosomes (SMC) family member, chromosome-ass S0564 phosphatidyl- 9791KIAA0024; PSSA; PTDSS1; DDVNYKM N/A N/A 1:1000- serinephosphatidylserine synthase 1 HFRMINEQ 1:8000 synthase 1 QVED (359)S0565 polo-like   5347 2.7.1.-; PLK1; STPK13; polo-like ENPLPERPR N/AN/A 1:10- kinase 1  kinase (Drosophila); polo  EKEEPVVR 1:100(Drosophila) (Drosophia)-like kinase; SERINE/ (360)THREONINE PROTEIN KINASE 13;  polo-like kinase 1 (Drosophila) S0567Pirin 8544 Pirin; PIR REQSEGVG N/A N/A 1:240 ARVRRSIG RPE (361) S0578ATP-binding  21 ABCA3; ABC3; LBM180; ABC-C; PRAVAGKE N/A N/A 1:1500cassette, sub- EST111653; ABC transporter 3; ATP- EEDSDPEK family A binding cassette 3; ATP-BINDING ALR (362) (ABC1), member CASSETTE TRANSPORTER 3; 3 ATP-BINDING CASSETTE,SUBFAMILY A, MEMBER 3; ATP- binding cassette, sub-family A member 3; ATP-binding cassette, sub- family A (ABC1), memb S0579ATP-binding   10347 ABCX; ABCA7; ABCA-SSN; EKADTDME N/A N/A 1:300-cassette, sub- autoantigen SS-N; macrophage ABC GSVDTRQE 1:400 family A transporter; SJOGREN SYNDROME K (363) (ABC1), member ANTIGEN SS-N; ATP-BINDING 7 CASSETTE, SUBFAMILY A,MEMBER 7; ATP-binding cassette, sub-family A (ABC1), member 7;ATP-binding cassette, sub-family A, member 7 isoform a; A S0581ATP-binding  22 ABCB7; Atm1p; ASAT; ABC7; RVQNHDNP N/A N/A 1:4000-cassette, sub- EST140535; ABC TRANSPORTER 7; KWEAKKE 1:10000family B (MDR/ ATP-binding cassette 7; ATP- NISK (364) TAP), member 7BINDING CASSETTE TRANSPORTER 7; Anemia,sideroblastic, with spinocerebellar ataxia; ATP-BINDING CASSETTE,SUBFAMILY B, MEMBER 7; ATP- binding cassette, sub-family B, member S0585ATP-binding  94160 MRP9; ABCC12; MULTIDRUG RSPPAKGA N/A N/A 1:500cassette, sub- RESISTANCE-ASSOCIATED TGPEEQSD family C (CFTR/PROTEIN 9; ATP-BINDING SLK (365) MRP), member 12 CASSETTE, SUBFAMILY C,MEMBER 12; ATP-binding cassette, sub-family C (CFTR/MRP), member 12S0586 ATP-binding  9429 ABC15; MXR1; ABCP; EST157481; REEDFKAT N/A N/A1:333- cassette, sub- MRX; ABCG2; BCRP1; BMDP; EIIEPSKQD 1:400family G   MITOXANTRONE-RESISTANCE KP (366) (WHITE),PROTEIN; mitoxantrone resistance member 2 protein; placenta specific MDRprotein; ATP-BINDING CASSETTE TRANSPORTER, PLACENTA-SPECIFIC; breast cancer resistance protein; ATP-BINDING CASS S0593solute carrier   28234 OATP1B3; SLC21A8; OATP8; DKTCMKW N/A N/A 1:500-organic anion  SLCO1B3; ORGANIC ANION STNSCGAQ 1:2400 transporterTRANSPORTER 8; solute carrier (367) family,organic anion transporter family, member 1B3 member 1B3; SOLUTE CARRIERFAMILY 21, MEMBER 8 (ORGANIC ANION TRANSPORTER); solute carrierfamily 21 (organic anion  transporter), member 8 S0597 solute carrier 9356 ROAT1; MGC45260; HOAT1; PAHT; DANLSKNG N/A N/A 1:3000 family 22 SLC22A6; PAH TRANSPORTER; GLEVWL (organic anionpara-aminohippurate transporter;  (368) transporter),renal organic anion transporter 1;  member 6solute carrier family 22 member 6  isoform b; solute carrier family 22member 6 isoform c; solute carrier  family 22 member 6 isoform S0604solute carrier  7355 UGT2; UGTL; UGAT; SLC35A2; EPFLPKLLT N/A N/A 1:2400family 35  UGT1; UDP-galactose translocator; K (369) (UDP-galactoseUDP-GALACTOSE TRANSPORTER, ISOFORM  transporter),2; UGALT UDP-GALACTOSE TRANSPORTER, member A2ISOFORM 1; solute carrier family 35 (UDP-galactose transporter), member A2; solute carrier family 35 (UDP-galactose transpo    S0607cell division  994 3.1.3.48; CDC25B; cell division  RKSEAGSG N/A N/A1:1800 cycle 25B cycle 25B; cell division cycle 25B    AASSSGEDisoform 4;   KEN (370) cell division cycle 25B isoform 5; cell division cycle 25B isoform 1;cell division cycle 25B isoform 2;  cell division cycle 25B isoform 3S0609 stearoyl-CoA 6319 SCD; acyl-CoA desaturase; stearoyl- DDIYDPTY N/AN/A 1:2000- desaturase  CoA desaturase (delta-9-desaturase); KDKEGPSP1:5000 (delta- fatty acid desaturase KVE (371) 9-desaturase) S0611mitogen- 6300 SAPK3; p38gamma; SAPK-3; p38- QSDEAKNN N/A N/A 1:100activated  GAMMA; PRKM12; MAPK12; MKGLPELE proteinERK3; ERK6; EXTRACELLULAR KKD (372) kinase 12 SIGNAL-REGULATED KINASE 6;mitogen-activated protein kinase 3; stress-activated protein kinase 3;mitogen-activated protein kinase 12 S0612 nuclear factor  4791LYT-10; LYT10; NFKB2; SRPQGLTE N/A N/A 1:4500 of kappa lightONCOGENE LYT 10; AEQRELEQ polypeptide  TRANSCRIPTION FACTOR NFKB2;EAK (373) gene enhancer   NFKB, p52/p100 SUBUNIT; in B-cells 2 LYMPHOCYTE TRANSLOCATION (p49/p100) CHROMOSOME 10; NUCLEARFACTOR KAPPA-B, SUBUNIT 2; Nuclear factor of kappa light chaingene enhancer in B-cells 2; nuclear factor of kappa 1 S0613tumor necrosis   958 Bp50; TNFRSF5; MGC9013; RVQQKGTS N/A N/A 1:250-factor receptor  CDW40; CD40 antigen; CD40L ETDTIC 1:270 superfamily,receptor; B CELL-ASSOCIATED (374) member 5 MOLECULE CD40; CD40 type IIisoform; B cell surface antigen  CD40; nerve growth factor receptor-related B-lymphocyte   activation molecule; tumor necrosisfactor receptor superfam S0614 Epstein-Barr  10148EBI3; IL27, EBI3 SUBUNIT; VRLSPLAE N/A N/A 1:1200- virus induced EPSTEIN-BARR VIRUS-INDUCED RQLQVQW 1:3000 gene 3GENE 3; INTERLEUKIN 27, EBI3 E (375) SUBUNIT; Epstein-Barr virus inducedgene 3; Epstein-Barr virus induced gene 3 precursor S0616 zinc finger 58495 ZNF339; zinc finger protein 339 RRSLGVSV N/A N/A 1:2500protein 339 RSWDELPD EKR (376) S0617 DAB2  153090DAB2IP; DAB2 interacting protein DEGLGPDP N/A N/A 1:600 interactingPHRDRLRS protein K (377) S0618 protein  8500MGC26800; LIP1; PPFIA1; LIP.1; SGKRSSDG N/A N/A 1:150 tyrosine LAR-interacting protein 1; PTPRF SLSHEEDL phosphatase, interacting protein alpha 1 isoform   AK (378) receptor type, a; PTPRF interacting protein alpha  f polypeptide 1 isoform b; protein tyrosine (PTPRF), phosphatase, receptor type, finteracting  polypeptide (PTPRF), interacting proteinprotein (liprin), alpha 1 (liprin), alpha 1 S0631 RGM domain  56963RGMA; REPULSIVE GUIDANCE SQERSDSPE N/A N/A 1:600 family,MOLECULE; RGM domain family, ICHYEKSFH member A member A K (379) S0633hypothetical  144347 LOC144347; hypothetical protein KVNPEPTH N/A N/A1:100- protein LOC144347 EIRCNSEVK 1:200 LOC144347 (380) S0639tetratrico- 57217 TTC7; tetratricopeptide repeat  RELREVLR N/A N/A1:2000- peptide repeat  domain 7 TVETKATQ 1:3000 domain 7 N (381) S0640protein C  5624 PROC; 3.4.21.69; PROC RDTEDQED N/A N/A 1:1000-(inactivator  DEFICIENCY PROTEIN C; QVDPRLID 1:1800 of coagulation THROMBOPHILIA, HEREDITARY, GK (382) factors DUE TO PC DEFICIENCY;Va and VIIIa) PROTEIN C DEFICIENCY, CONGENITAL THROMBOTICDISEASE DUE TO; protein C (inactivator of coagulation factors Va and VIIIa) S0643 transducin-like 7090 HsT18976; KIAA1547; ESG3; TLE3;KNHHELDH N/A N/A 1:200- enhancer of  transducin-like enhancer protein 3;  RERESSAN 1:1440 split 3 (E(sp1)enhancer of split groucho 3; (383) homolog,transducin-like enhancer of split 3 Drosophila)(E(sp1) homolog, Drosophila) S0645 frizzled   8324FzE3; FZD7; frizzled 7; frizzled SDGRGRPA N/A N/A 1:900 homolog 7 homolog 7 (Drosophila); Frizzled, FPFSCPRQ (Drosophila)drosophila, homolog of, 7 (384) S0646 solute carrier 6520MDUl; 4T2HC; SLC3A2; NACAE; GSKEDFDS N/A N/A 1:3600- family 3   4F2HC; 4F2 HEAVY CHAIN; CD98 LLQSAKK 1:5400 (activators of   HEAVY CHAIN; CD98 (385) dibasic and   MONOCLONAL ANTIBODY 44D7;neutral amino ANTIGEN DEFINED BY acid  MONOCLONAL ANTIBODY 4F2,transport), HEAVY CHAIN; antigen identified by member 2monoclonal antibodies 4F2, TRA1.10, TROP4, and T43; SOLUTECARRIER FAMILY 3 S0648 KIAA0738 gene 9747KIAA0738; KIAA0738 gene product EYRNQTNL N/A N/A 1:200 product PTENVDK(386) S0651 phospholipase  22925 PLA2IR; PLA2-R; PLA2R1; QKEEKTW N/A N/A1:3600 A2 receptor 1,   PLA2G1R; PHOSPHOLIPASE A2 HEALRSCQ 180 kDaRECEPTOR, 180-1 (D; phospholipase ADN (387) A2 receptor 1, 180 kDa S0654KIAA0182  23199 KIAA0182; KIAA0182 protein EKAEEGPR N/A N/A 1:400protein KREPAPLD K (388) S0659 thymidine   7084 TK2; THYMIDINE KINASE,EQNRDRIL N/A N/A 1:300 kinase 2,  MITOCHONDRIAL; thymidine TPENRKmitochondrial kinase 2, mitochondrial (389) S0663 chromosome 14  64430C14orf135; chromosome 14 open RDWYIGLV N/A N/A 1:900 open reading reading frame 135 SDEKWK frame 135 (390) S0665 KIAA1007  23019KIAA1007; KIAA1007 protein; DSYLKTRS N/A N/A 1:1500- proteinadrenal gland protein AD-005; PVTFLSDLR 1:3000KIAA1007 protein isoform a; (391) KIAA1007 protein isoform b S0670DKFZP566O1646 25936 DC8; DKFZP56601646 protein KCRGETVA N/A N/A 1:900protein KEISEAMK S (392) S0672 B-cell 605BCL7A; B-cell CLL/lymphoma-7; B- QRGSQIGR N/A N/A 1:800 CLL/lymphoma cell CLL/lymphoma 7A EPIGLSGD 7A (393) S0673 likely ortholog  28987ART-4; NOB1P; adenocarcinoma KPPQETEK N/A N/A 1:50 of mouse nin antigen recognized by T lymphocytes  GHSACEPE one binding 4; likely ortholog of mouse nin one  N (394) protein binding proteinS0676 guanine  2768 RMP; NNX3; GNA12; GUANINE ERRAGSGA N/A N/A 1:1200-nucleotide NUCLEOTIDE-BINDING PROTEIN, RDAERE 1:2400 binding proteinALPHA-12; guanine nucleotide (395) (G protein)binding protein (G protein) alpha  alpha 12 12 S0677 GrpE-like 1, 80273HMGE; GRPEL1; HUMAN SEQKADPP N/A N/A 1:500- mitochondrial MITOCHONDRIAL GrpE PROTEIN; ATEKTLLE 1:1000 (E. coli)GrpE-like 1, mitochondrial (E.   (396)coli); GrpE, E. COLI, HOMOLOG OF, 1 S0684 hypothetical  91607FLJ34922; hypothetical protein EAEWSQGV N/A N/A 1:8100 protein FLJ34922QGTLRIKK FLJ34922 YLT (397) S0687 hypothetical  54942FLJ20457; hypothetical protein EESKSITEG N/A N/A 1:600- protein FLJ20457LLTQKQYE 1:1260 FLJ20457 (398) S0691 solute carrier  23657CCBR1; SLC7A11; xCT; QNFKDAFS N/A N/A 1:1000- family 7, cystine/glutamate transporter; GRDSSITR 1:1575 (cationic amino SYSTEM Xc(−) TRANSPORTER- (399) acid   RELATED PROTEIN; SOLUTEtransporter, CARRIER FAMILY 7, MEMBER 11; y+ system)solute carrier family 7, (cationic  member 11 amino acid transporter, y+system)  member 11 S0692 glutamate- 2729 GLCLC; GCLC; 6.3.2.2; GCS;EKIHLDDA N/A N/A 1:100- cysteine GAMMA-GLUTAMYLCYSTEINE NESDHFEN 1:400ligase,  SYNTHETASE, CATALYTIC (400) catalyticSUBUNIT; glutamate-cysteine ligase, subunit catalytic subunit S0695integrin,  3691 ITGB4; INTEGRIN, BETA-4; TEDVDEFR N/A N/A 1:2700- beta 4integrin, beta 4 NKLQGER 1:4050 (401) S0702 solute carrier   8140SLC7A5; MPE16; D16S469E; CD98; KGDVSNLD N/A N/A 1:21160- family 7   LAT1; 4F2 light chain; Membrane PNFSFEGTK 1:178200 (cationic aminoprotein E16; L-TYPE AMINO ACID LDV (402) acid    TRANSPORTER 1; Solute carrier transporter, family 7, member 5; solute carrier y+ system),family 7 (cationic amino acid member 5 transporter, y+ system), member 5S0705 breast cancer 25855 DKFZp564A063; BRMS1; breast KARAAVSP N/A N/A1:1000- metastasis  cancer metastasis-suppressor 1;   QKRKSDGP 1:2000suppressor 1 breast cancer metastasis  (403) suppressor 1 S0706 KiSS-1 3814 MGC39258; KISS1; KiSS-1 RQIPAPQG N/A N/A 1:180 metastasis-metastasis-suppressor; KISS1 AVLVQREK suppressorMETASTIN; malignant melanoma D (404) metastasis-suppressor; KISS1METASTASIS SUPPRESSOR S0708 cofactor   9439DKFZp434H0117; CRSP133; SUR2; SVKEQVEK N/A N/A 1:2430 required for DRIP130; CRSP3; mediator; IICNLKPAL Sp1    transcriptional co-activator K (138) transcriptional  CRSP130; CRSP, 130-KD SUBUNIT;  activation,CRSP 130-kD subunit; 133 kDa subunit 3,transcriptional co-activator; 130  130 kDakDa transcriptional co-activator;  vitamin D3 receptor interacting protein; c S5002 keratin 14 3861 CK; KRT14; K14; EBS4; EBS3;Antibody obtained from  1:50 (epidermolysis cytokeratin 14; CK 14; KERATIN, Chemicon bullosa  TYPE I CYTOSKELETAL 14; keratin simplex, 14 (epidermolysis bullosa simplex, Dowling-Meara,Dowling-Meara, Koebner) Koebner) S5003 keratin 17 3872PCHC1; PC; PC2; 39.1; KRT17; K17; Antibody obtained from  1:10-CYTOKERATIN 17; VERSION 1; Dako 1:25 CK 17; KERATIN, TYPE ICYTOSKELETAL 17 S5004 keratin 18 3875 K18; CYK18; KRT18;Antibody obtained from  1:200- CYTOKERATIN 18; CK 18; Dako 1:400KERATIN, TYPE I CYTOSKELETAL 18 S5005 keratin 18 3875 K18; CYK18; KRT18;Antibody obtained from  1:50- CYTOKERATIN 18; CK 18; Becton Dickinson1:100 KERATIN, TYPE I CYTOSKELETAL 18 S5012 tumor- 4072TROP1; LY74; Ep-CAM; GA733-2; Antibody obtained from  1:40 associatedEGP40; MK-1; CO17-1A; EPCAM; Oncogene Research  calcium signalM4S1; KSA; TACSTD1; EGP; MK-1 Products (Calbiochem) transducer 1antigen; EPITHELIAL CELLULAR ADHESION MOLECULE; GASTROINTESTINAL TUMOR-ASSOCIATED ANTIGEN 2, 35-KD GLYCOPROTEIN; tumor-associatedcalcium signal transducer 1  precurso S5014 estrogen   2100ER-BETA; ESR-BETA; ESR2; Erb; Antibody obtained from  1:2500 receptorESRB; NR3A2; ESTROGEN Oncogene Research   2 (ER beta)RECEPTOR, BETA; estrogen receptor Products (Calbiochem) 2 (ER beta)S5038 mucin 1, 4582 PEMT; MUC1; episialin; EMA; PUM; Antibody obtained from  1:1 transmembrane H23AG; CD227; PEM;Imperial Cancer Research  CARCINOMA-ASSOCIATED Technology (ICRT)MUCIN; H23 antigen; TUMOR- ASSOCIATED MUCIN; DF3 antigen;peanut-reactive urinary mucin;  mucin 1, transmembrane; polymorphic epithelial mucin; MUCIN 1, URINARY; MUCIN,  TUMOR-ASSOCIATES5044 transferrin   7037 P90; TR; TFRC; TFR; CD71; T9;Antibody obtained from  1:20 receptor TRFR; ANTIGEN CD71; NeoMarkers(p90, CD71) TRANSFERRIN RECEPTOR PROTEIN; transferrin receptor (p90,CD71) S5045 v-erb-b2 2064 HER-2; ERBB2; NGL; P185ERBB2;Antibody obtained from  1:600 erythroblasticHER2; C-ERBB-2; NEU; MLN 19; NeoMarkers leukemia viralEC 2.7.1.112; TKR1 HERSTATIN; oncogene  NEU PROTO-ONCOGENE; homolog 2, ONCOGENE ERBB2; RECEPTOR neuro/ PROTEIN-TYROSINE KINASE glioblastomaERBB-2 PRECURSOR; ONCOGENE derived  NGL, NEUROBLASTOMA-OR oncogeneGLIOBLASTOMA-DERIVED; homolog (avian) TYROSINE KINASE-TYPE CELL S5047major vault  9961 MVP; LRP; VAULT1; LUNG Antibody obtained from  1:300protein RESISTANCE-RELATED PROTEIN; NeoMarkers MAJOR VAULT PROTEIN, RAT,HOMOLOG OF S5064 tumor protein  8626 LMS; TP73L; KET; SHFM4; p73H;Antibody obtained from  1:50 p73-like EEC3; TP63; p51; TUMOR PROTEINDako p63; TUMOR PROTEIN p73-LIKE; p53-RELATED PROTEIN p63; tumorprotein 63 kDa with strong homology to p53 S5065 estrogen   2099ER; NR3A1; ESR1; Era; ESR; ER- Antibody obtained from  1:20 receptor 1ALPHA; ESRA; ESTRADIOL Dako RECEPTOR; ESTROGEN RECEPTOR, ALPHA; estrogenreceptor 1 (alpha) S5066 v-erb-b2 2064 HER-2; ERBB2; NGL; P185ERBB2;Antibody obtained from  1:300 erythroblasticHER2; C-ERBB-2; NEU; MLN 19; Dako leukemia viralEC 2.7.1.112; TKR1 HERSTATIN; oncogene   NEU PROTO-ONCOGENE; homologONCOGENE ERBB2; RECEPTOR 2, neuro/ PROTEIN-TYROSINE KINASE glioblastomaERBB-2 PRECURSOR; ONCOGENE derived  NGL, NEUROBLASTOMA-OR oncogeneGLIOBLASTOMA-DERIVED; homolog (avian) TYROSINE KINASE-TYPE CELL S5067cathepsin D 1509 CTSD; MGC2311; CPSD; EC Antibody obtained from  1:20-(lysosomal  3.4.23.5; cathepsin D preproprotein; Dako 1:50 aspartylCathepsin D precursor; cathepsin D protease)(lysosomal aspartyl protease); S5069 CA 125 n/a Antibody obtained from 1:20 Dako S5070 CA 15-3 n/a Antibody obtained from  1:50 Dako S5071CA 19-9 n/a Antibody obtained from  1:50 Dako S5072 v-myc 4609c-Myc; MYC; ONCOGENE MYC; Antibody obtained from  1:50 myelocyto-Myc proto-oncogene protein; Dako matosis PROTOONCOGENE viral oncogeneHOMOLOGOUS TO homolog (avian) MYELOCYTOMATOSIS VIRUS; v-myc myelocytomatosis viral  oncogene homolog (avian); v-myc avian myelocytomatosis  viral oncogene homolog; Avian myelocytomatosis viral (v-myc)  onco S5073 cadherin 1, type 999CDH1; Cadherin-1; Arc-1; ECAD; Antibody obtained from  1:100-1, E-cadherin  CDHE; Uvomorulin; LCAM; Dako 1:150 (epithelial)Epithelial-cadherin precursor;  cell-CAM 120/80; CADHERIN,EPITHELIAL; calcium-dependent adhesion protein,  epithelial; cadherin 1, E-cadherin   (epithelial); cadherin 1, type 1  preproprotein; cadherin 1, S5074 glutathione S- 2950GSTP1; DFN7; GSTP1-1; GST3; Antibody obtained from  1:50 transferase piGSTPP; GST class-pi; glutathione Dako transferase; EC 2.5.1.18; glutathione S-transferase pi; GST,  CLASS PI; deafness, X-linked 7;GLUTATHIONE S-TRANSFERASE 3; GLUTATHIONE S- TRANSFERASE, PI; FAEES3GLUTATHIONE S-TRANSFERASE PI PSEUD S5075 tumor protein 7157p53; TP53; TRP53; Antibody obtained from  1:50 p53 (Li-FraumeniPHOSPHOPROTEIN P53; Dako syndrome) TRANSFORMATION-RELATEDPROTEIN 53; TUMOR SUPPRESSOR P53; CELLULAR TUMOR ANTIGEN P53; tumorprotein p53 (Li-Fraumeni syndrome) S5076 progesterone  5241NR3C3; PR; PGR; PROGESTERONE Antibody obtained from  1:50 receptorRESISTANCE; PSEUDOCORPUS Dako LUTEUM INSUFFICIENCY PROGESTERONE RECEPTORS5077 trefoil factor 7031 Antibody obtained from  1:50- 1 (breast   Dako1:100 cancer,  estrogen-    inducible sequence expressed in) S5079enolase 2,  2026 NSE; ENO2; 2-phospho-D-glycerateAntibody obtained from  1:400 (gamma,  hydro-lyase; ENOLASE, GAMMA; Dakoneuronal) neurone-specific enolase; ENOLASE,NEURON-SPECIFIC; 2-phospho-D- glycerate hydrolyase; EC 4.2.1.11;Neural enolase; enolase-2, gamma, neuronal; neuron specific gammaenolase; enolase 2, (gamma, S5080 B-cell 596 BCL2; FOLLICULAR LYMPHOMA;Antibody obtained from  1:50 CLL/lymphoma 2 APOPTOSIS REGULATOR BCL-2;Dako B-cell CLL/lymphoma 2; B-cell lymphoma protein 2 alpha; B-celllymphoma protein 2 beta; ONCOGENE B-CELL LEUKEMIA 2 LEUKEMIA, CHRONICLYMPHATIC, TYPE 2 S5081 retinoblastoma 1 5925p105-Rb; PP110; Retinoblastoma-1; Antibody obtained from  1:20(including RB; RB1; RETINOBLASTOMA- Dako osteosarcoma)ASSOCIATED PROTEIN; RB OSTEOSARCOMA, RETINOBLASTOMA-RELATED;retinoblastoma 1 (including osteosarcoma) S5082 synaptophysin 6855SYP; Synaptophysin; Major synaptic Antibody obtained from  1:50vesicle protein P38 Dako S5083 BCL2-associated 581BAX; BCL2-associated X protein; Antibody obtained from  1:500 X proteinAPOPTOSIS REGULATOR BAX, Dako MEMBRANE ISOFORM ALPHA S5086 estrogen  2100 ER-BETA; ESR-BETA; ESR2; Erb; Antibody obtained from  1:200receptor ESRB; NR3A2; ESTROGEN Abcam 2 (ER beta)RECEPTOR, BETA; estrogen receptor 2 (ER beta) S5087 mucin 1, 4582PEMT; MUC1; episialin; EMA; PUM;   Antibody obtained from  1:200-transmembrane H23AG; CD227; PEM; CARCINOMA- Zymed 1:1600ASSOCIATED MUCIN; H23 antigen;  TUMOR-ASSOCIATED MUCIN; DF3antigen; peanut-reactive urinary mucin; mucin 1, transmembrane;polymorphic epithelial mucin;  MUCIN 1, URINARY; MUCIN, TUMOR- ASSOCIATES6001 estrogen   2099 ER; NR3A1; ESR1; Era; ESR; ER-Antibody obtained from  1:1 receptor 1 ALPHA; ESRA; ESTRADIOL US LabsRECEPTOR; ESTROGEN RECEPTOR, ALPHA; estrogen receptor 1 (alpha) S6002progesterone  5241 NR3C3; PR; PGR; PROGESTERONE Antibody obtained from 1:1 receptor RESISTANCE; PSEUDOCORPUS US Labs LUTEUM INSUFFICIENCYPROGESTERONE RECEPTOR S6003 v-erb-b2 2064 HER-2; ERBB2; NGL; P185ERBB2;Antibody obtained from  1:1 erythroblastic HER2; C-ERBB-2; NEU; MLN 19;US Labs leukemia viral EC 2.7.1.112; TKR1 HERSTATIN; oncogene homologNEU PROTO-ONCOGENE; 2, neuro/ ONCOGENE ERBB2; RECEPTOR glioblastomaPROTEIN-TYROSINE KINASE derived oncogene ERBB-2 PRECURSOR; ONCOGENEhomolog (avian) NGL, NEUROBLASTOMA-OR GLIOBLASTOMA-DERIVED;TYROSINE KINASE-TYPE CELL S6004 B-cell 596 BCL2; FOLLICULAR LYMPHOMA;Antibody obtained from  1:1 CLL/lymphoma 2 APOPTOSIS REGULATOR BCL-2;US Labs B-cell CLL/lymphoma 2; B-cell lymphoma protein 2 alpha; B-celllymphoma protein 2 beta; ONCOGENE B-CELL LEUKEMIA 2 LEUKEMIA, CHRONICLYMPHATIC, TYPE 2 S6005 keratin 5 3852 KRT5; EBS2; Keratin-5; K5;Antibody obtained from  1:1 (epidermolysis  CYTOKERATIN 5; CK 5; 58 KDAUS Labs bullosa simplex, CYTOKERATIN; KERATIN, TYPE Dowling-Meara/II CYTOSKELETAL 5; keratin 5 Kobner/Weber-(epidermolysis bullosa simplex, Cockayne types)Dowling-Meara/Kobner/Weber- Cockayne types) S6006 tumor protein   7157p53; TP53; TRP53; Antibody obtained from  1:1 p53 (Li-Fraumeni PHOSPHOPROTEIN P53; US Labs syndrome) TRANSFORMATION-RELATEDPROTEIN 53; TUMOR SUPPRESSOR P53; CELLULAR TUMOR ANTIGEN P53; tumorprotein p53 (Li-Fraumeni syndrome) S6007 KI67 n/aAntibody obtained from  1:1 US Labs S6008 epidermal growth 1956S7; EGFR; 2.7.1.112; ERBB; Antibody obtained from  1:1 factor receptorONCOGENE ERBB; ERBB1 US Labs (erythroblastic SPECIES ANTIGEN 7; V-ERB-Bleukemia viral  AVIAN ERYTHROBLASTIC (v-erb-b)   LEUKEMIA VIRAL ONCOGENEoncogene HOMOLOG; epidermal growth factor homolog, avian)receptor (avian erythroblastic  leukemia viral (v-erb-b) oncogenehomolog) S6011 enolase 2,  2026 NSE; ENO2; 2-phospho-D-glycerateAntibody obtained from  1:1 (gamma,  hydro-lyase; ENOLASE, GAMMA;US Labs neuronal) neurone-specific enolase; ENOLASE,NEURON-SPECIFIC; 2-phospho-D- glycerate hydrolyase; EC 4.2.1.11;Neural enolase; enolase-2, gamma, neuronal; neuron specific gammaenolase; enolase 2, (gamma, S6012 thyroid  7080benign chorea; chorea, hereditary   Antibody obtained from   1:1transcription benign; NK-2 (Drosophila) homolog A  US Labs factor 1(thyroid nuclear factor); Thyroid transcription factor 1 (NK-2, Drosophila, homolog of, A);  BCH; BHC; TEBP; TTF1;  NKX2A; TTF-1; NKX2.1S6013 v-erb-b2 2064 HER-2; ERBB2; NGL; P185ERBB2; Antibody obtained from  1:1 erythroblastic HER2; C-ERBB-2; NEU; MLN 19;US Labs leukemia viral EC 2.7.1.112; TKR1 HERSTATIN; oncogene homolog NEU PROTO-ONCOGENE; 2, neuro/ ONCOGENE ERBB2; RECEPTOR glioblastomaPROTEIN-TYROSINE KINASE derived oncogene ERBB-2 PRECURSOR; ONCOGENEhomolog (avian) NGL, NEUROBLASTOMA-OR GLIOBLASTOMA-DERIVED;TYROSINE KINASE-TYPE CELL

Other Embodiments

Other embodiments of the invention will be apparent to those skilled inthe art from a consideration of the specification or practice of theinvention disclosed herein. It is intended that the specification andexamples be considered as exemplary only, with the true scope of theinvention being indicated by the following claims.

We claim:
 1. A method of identifying a breast cancer that will respondfavorably to a chemotherapy treatment that includes a taxane or taxanederivative, the method comprising: (a) performing immunohistochemicalstaining for TLE3 polypeptide on a cancer sample obtained from a breastcancer patient, wherein the breast cancer patient is triple negative forestrogen receptor, progesterone receptor, and HER-2 markers; (b)detecting a percentage and/or intensity of immunohistochemical stainingfor TLE3 polypeptide in the cancer sample, wherein the detectedpercentage and/or intensity is higher than a reference; and (c)identifying the patient's breast cancer as one that will respondfavorably to a chemotherapy treatment that includes a taxane or taxanederivative, wherein the step of performing immunohistochemical stainingcomprises contacting the cancer sample with an antibody that binds TLE3polypeptide thereby forming a complex comprising the antibody and TLE3polypeptide, and the step of detecting comprises detecting the complexin the cancer sample.
 2. The method of claim 1, wherein the step ofdetecting comprises quantifying a percentage of cells in whichimmunohistochemical staining for TLE3 polypeptide is detected.
 3. Themethod of claim 1 wherein the step of detecting comprises quantifying anintensity of immunohistochemical staining for TLE3 polypeptide in thecancer sample.
 4. The method of claim 1, wherein the step of identifyingcomprises identifying the patient's breast cancer as one that willrespond favorably to a chemotherapy treatment that includes a taxane. 5.The method of claim 4, wherein the taxane is paclitaxel or docetaxel. 6.The method of claim 1, further comprising administering a chemotherapytreatment that includes a taxane or taxane derivative to the breastcancer patient.
 7. A method of identifying a breast cancer that willrespond favorably to a chemotherapy treatment that includes a taxane ortaxane derivative, the method comprising: (a) performingimmunohistochemical staining for TLE3 polypeptide on a cancer sampleobtained from a breast cancer patient, wherein the breast cancer patientis triple negative for estrogen receptor, progesterone receptor, andHER-2 markers; (b) detecting a percentage and/or intensity ofimmunohistochemical staining for TLE3 polypeptide in the cancer sample,wherein the detected percentage and/or intensity is higher than areference; and (c) identifying the patient's breast cancer as one thatwill respond favorably to a chemotherapy treatment that includes ataxane or taxane derivative, wherein the step of performingimmunohistochemical staining comprises contacting the cancer sample witha primary antibody that binds TLE3 polypeptide and a labeled secondaryantibody that binds the primary antibody thereby forming a complexcomprising the primary antibody, secondary antibody and TLE3polypeptide, and the step of detecting comprises detecting the complexin the cancer sample.
 8. A method of predicting the likelihood that abreast cancer will respond to a chemotherapy treatment that includes ataxane or taxane derivative, the method comprising: (a) performingimmunohistochemical staining for TLE3 polypeptide on a cancer sampleobtained from a breast cancer patient, wherein the breast cancer patientis triple negative for estrogen receptor, progesterone receptor, andHER-2 markers; (b) detecting a percentage and/or intensity ofimmunohistochemical staining for TLE3 polypeptide in the cancer sample,wherein the detected percentage and/or intensity is higher than areference; and (c) predicting that the patient's breast cancer willlikely respond to a chemotherapy treatment that includes a taxane ortaxane derivative, wherein the step of performing immunohistochemicalstaining comprises contacting the cancer sample with an antibody thatbinds TLE3 polypeptide thereby forming a complex comprising the antibodyand TLE3 polypeptide, and the step of detecting comprises detecting thecomplex in the cancer sample.
 9. The method of claim 8, wherein the stepof detecting comprises quantifying a percentage of cells in whichimmunohistochemical staining for TLE3 polypeptide is detected.
 10. Themethod of claim 8, wherein the step of detecting comprises quantifyingan intensity of immunohistochemical staining for TLE3 polypeptide in thecancer sample.
 11. The method of claim 8, wherein the step of predictingcomprises predicting that the patient's breast cancer will likelyrespond to a chemotherapy treatment that includes a taxane.
 12. Themethod of claim 11, wherein the taxane is paclitaxel or docetaxel. 13.The method of claim 8 further comprising administering a chemotherapytreatment that includes a taxane or taxane derivative to the breastcancer patient.
 14. A method of predicting the likelihood that a breastcancer will respond to a chemotherapy treatment that includes a taxaneor taxane derivative, the method comprising: (a) performingimmunohistochemical staining for TLE3 polypeptide on a cancer sampleobtained from a breast cancer patient, wherein the breast cancer patientis triple negative for estrogen receptor, progesterone receptor, andHER-2 markers; (b) detecting a percentage and/or intensity ofimmunohistochemical staining for TLE3 polypeptide in the cancer sample,wherein the detected percentage and/or intensity is higher than areference; and (c) predicting that the patient's breast cancer willlikely respond to a chemotherapy treatment that includes a taxane ortaxane derivative, wherein the step of performing immunohistochemicalstaining comprises contacting the cancer sample with a primary antibodythat binds TLE3 polypeptide and a labeled secondary antibody that bindsthe primary antibody thereby forming a complex comprising the primaryantibody, secondary antibody and TLE3 polypeptide, and the step ofdetecting comprises detecting the complex in the cancer sample.
 15. Amethod of treating a breast, lung or ovarian cancer patient, the methodcomprising: (a) performing immunohistochemical staining for TLE3polypeptide on a cancer sample obtained from a breast, lung or ovariancancer patient; (b) detecting a percentage and/or intensity ofimmunohistochemical staining for TLE3 polypeptide in the cancer sample,wherein the detected percentage and/or intensity is higher than areference; and (c) administering a chemotherapy treatment that includesa taxane or taxane derivative to the patient, wherein the step ofperforming immunohistochemical staining comprises contacting the cancersample with an antibody that binds TLE3 polypeptide thereby forming acomplex comprising the antibody and TLE3 polypeptide and the step ofdetecting comprises detecting the complex in the cancer sample.
 16. Themethod of claim 15, wherein the step of detecting comprises quantifyinga percentage of cells in which immunohistochemical staining for TLE3polypeptide is detected.
 17. The method of claim 15, wherein the step ofdetecting comprises quantifying an intensity of immunohistochemicalstaining for TLE3 polypeptide in the cancer sample.
 18. The method ofclaim 15, wherein the cancer sample is obtained from a breast cancerpatient.
 19. The method of claim 15, wherein the step of administeringcomprises administering a taxane.
 20. The method of claim 19, whereinthe taxane is paclitaxel or docetaxel.
 21. The method of claim 18,wherein the breast cancer patient is triple negative for estrogenreceptor, progesterone receptor, and HER-2 markers.
 22. The method ofclaim 15, wherein the cancer sample is obtained from a lung cancerpatient.
 23. The method of claim 22, wherein the step of administeringcomprises administering a taxane.
 24. The method of claim 23, whereinthe taxane is paclitaxel or docetaxel.
 25. The method of claim 15,wherein the cancer sample is obtained from an ovarian cancer patient.26. The method of claim 25, wherein the step of administering comprisesadministering a taxane.
 27. The method of claim 26, wherein the taxaneis paclitaxel or docetaxel.
 28. A method of treating a breast, lung orovarian cancer patient, the method comprising: (a) performingimmunohistochemical staining for TLE3 polypeptide on a cancer sampleobtained from a breast, lung or ovarian cancer patient; (b) detecting apercentage and/or intensity of immunohistochemical staining for TLE3polypeptide in the cancer sample, wherein the detected percentage and/orintensity is higher than a reference; and (c) administering achemotherapy treatment that includes a taxane or taxane derivative tothe patient, wherein the step of performing immunohistochemical stainingcomprises contacting the cancer sample with a primary antibody thatbinds TLE3 polypeptide and a labeled secondary antibody that binds theprimary antibody thereby forming a complex comprising the primaryantibody, secondary antibody and TLE3 polypeptide; and the step ofdetecting comprises detecting the complex in the cancer sample.
 29. Themethod of claim 28, wherein the cancer sample is obtained from a breastcancer patient, and the taxane is paclitaxel or docetaxel.
 30. Themethod of claim 29, wherein the breast cancer patient is triple negativefor estrogen receptor, progesterone receptor, and HER-2 markers.